* AMBER Cornell et al. (parm94) force field conversion * See: JACS (1995) 117, 5179-5197. * converted by tec3, march 1997 * 23 1 ! NOTE: the charges here are un-scaled and represent the ! exact AMBER charges. ! ! Standard CHARMM residue names are utilized: ! ! ADE, THY, GUA, CYT, URA. ! ! Atom type names conform to the AMBER Cornell et. al. 1995, ! parm94.dat & all_nuc94.in naming conventions where possible. ! Exceptions to this rule include types with "*" in the name ! (i.e. N*->NS, C*->CS). CHARMM atom names are utilized. To build ! the residues, the BILD arrays from the top_all22_na.inp were ! utilized (since these are actually probably more trustworthy then ! those supplied in AMBER) and modified where necessary (i.e. THY). ! BONDS were also copied from top_all22_na.inp and all angles and ! dihedrals autogenerated. The impropers were taken straight from the ! all_nuc94.in. All this was done by hand editing. ! ! Results were checked by comparing energies and forces for all the ! residues defined herein. In general, in simulations performing a ! single energy and force evaluation with a cutoff large enough to ! span the entire system the energies and forces agree ! to within ~0.00005 using both CHARMM and AMBER. The AMBER energies ! and forces were calculated using AMBER 4.1/5.0_alpha sander ! (minimization or dynamics) and CHARMM c25n3 (ener). Note that ! differences in the forces may be apparent if the coordinates do not ! match exactly or in cases where different constants are used between ! AMBER and CHARMM. These points require a little more elaboration. ! ! Differences in the coordinates: ! ! (*) incorrect mapping between AMBER and CHARMM coordinates ! (i.e. not 1-to-1). This is possible with hand editting of the ! AMBER names to convert to CHARMM if the correct mapping isn't ! followed. The only case that was readily apparent in this ! analysis was incorrect mapping of H2' and H2'' in the DNA ! residues of ADE, GUA and CYT. The rename command can be used ! to swap names and alleviate this problem (which is not a real ! problem except when comparing forces). ! ! (*) parm coordinate precision. If the parm coordinates were ! created from a PDB file using the link-edit-parm path, improper ! conversion from text->binary->text in edit/parm leads to ! differences in the parm coordinates from the PDB file. ! Therefore, the coordinates will be different than those ! generated by CHARMM using the same PDB coordinates. Therefore, ! prior to comparing forces, the PDB should be converted directly ! to the parm coordinates (which can be done using carnal). ! ! Differences in the electrostatic energies: ! ! (*) The conversion from charge units to kcal/mol in CHARMM is based ! on the value 332.0716 whereas AMBER uses 18.2223**2 or 332.0522173. ! The actual value is somewhat lower than both these values ! (~331.843)! To convert the charges to "CHARMM", they should be ! multiplied by 1.000058372. This was not done within this file. ! [When this is done, the charges are not rounded and therefore ! non-integral charges for the residues are apparent.] To get around ! this problem either the charges can be scaled within CHARMM (which ! will still lead to non-integral charge) or in versions of CHARMM ! beyond c25n3, and through the application of the "AMBER" keyword in ! pref.dat, the AMBER constant can be used. By default, the "fast" ! routines cannot be used with the AMBER-style impropers. In the ! later versions of CHARMM, the AMBER keyword circumvents this ! problem. ! ! BUILDING NUCLEIC ACID STRUCTURES: ! ! To build residues, use the standard naming conventions. By default ! the 5ter and 3ter patchs are applied which convert the first ! residue to a 5'-hydroxyl (no terminal phosphate) and the last ! residue to a 3'-hydroxyl. ! ! NOTE that in the case of case of ADE, GUA and CYT, by default the ! system is RIBONUCLEIC acid. To convert to deoxyribose, use the ! following patchs: ! ! patch DOA5 segid residue <-- 5'-terminal ADE ! patch DOA segid residue <-- standard ADE ! patch DOA3 segid residue <-- 3'-terminal ADE ! patch DOC5 segid residue <-- 5'-terminal CYT ! patch DOC segid residue <-- standard CYT ! patch DOC3 segid residue <-- 3'-terminal CYT ! patch DOG5 segid residue <-- 5'-terminal GUA ! patch DOG segid residue <-- standard GUA ! patch DOG3 segid residue <-- 3'-terminal GUA ! ! ...where "segid" is the current segment and "residue" is the ! residue number ! ! As an example, let's build a single stranded DNA, d[CATG]. We need ! to apply 5' and 3' terminal patches and also patches to turn the ! RNA into DNA for each residue (except THY which is DNA). ! ! read sequence card ! 4 ! CYT ADE THY GUA ! generate s1 setup ! patch doc5 s1 1 ! patch doa s1 2 ! patch dog3 s1 4 ! ! ! Any problems? Let me know... ! cheatham@helix.nih.gov, cheatham@cgl.ucsf.edu ! ! ! ! AMBER atom types and masses (from all_nuc94.in) ! MASS 1 BR 79.90 ! bromine MASS 2 C 12.01 ! sp2 C carbonyl group MASS 3 CA 12.01 ! sp2 C pure aromatic (benzene) MASS 4 CB 12.01 ! sp2 aromatic C, 5&6 membered ring junction MASS 5 CC 12.01 ! sp2 aromatic C, 5 memb. ring HIS MASS 6 CK 12.01 ! sp2 C 5 memb.ring in purines MASS 7 CM 12.01 ! sp2 C pyrimidines in pos. 5 & 6 MASS 8 CN 12.01 ! sp2 C aromatic 5&6 memb.ring junct.(TRP) MASS 9 CQ 12.01 ! sp2 C in 5 mem.ring of purines between 2 N MASS 10 CR 12.01 ! sp2 arom as CQ but in HIS MASS 11 CT 12.01 ! sp3 aliphatic C MASS 12 CV 12.01 ! sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) MASS 13 CW 12.01 ! sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) MASS 14 CS 12.01 ! sp2 arom. 5 memb.ring w/1 subst. (TRP) MASS 15 C0 40.08 ! calcium MASS 16 H 1.008 ! H bonded to nitrogen atoms MASS 17 HC 1.008 ! H aliph. bond. to C without electrwd.group MASS 18 H1 1.008 ! H aliph. bond. to C with 1 electrwd. group MASS 19 H2 1.008 ! H aliph. bond. to C with 2 electrwd.groups MASS 20 H3 1.008 ! H aliph. bond. to C with 3 eletrwd.groups MASS 21 HA 1.008 ! H arom. bond. to C without elctrwd. groups MASS 22 H4 1.008 ! H arom. bond. to C with 1 electrwd. group MASS 23 H5 1.008 ! H arom. bond. to C with 2 electrwd. groups MASS 24 HO 1.008 ! hydroxyl group MASS 25 HS 1.008 ! hydrogen bonded to sulphur MASS 26 HW 1.008 ! H in TIP3P water MASS 27 HP 1.008 ! H bonded to C next to positively charged gr MASS 28 F 19.00 ! fluorine MASS 29 I 126.9 ! iodine MASS 30 IM 35.45 ! assumed to be Cl- MASS 31 IP 22.99 ! assumed to be Na+ MASS 32 IB 131.0 ! 'big ion w/ waters' for vacuum (Na+, 6H2O) MASS 33 MG 24.305 ! magnesium MASS 34 N 14.01 ! sp2 nitrogen in amide groups MASS 35 NA 14.01 ! sp2 N in 5 memb.ring w/H atom (HIS) MASS 36 NB 14.01 ! sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) MASS 37 NC 14.01 ! sp2 N in 6 memb.ring w/LP (ADE,GUA) MASS 38 N2 14.01 ! sp2 N in amino groups MASS 39 N3 14.01 ! sp3 N for charged amino groups (Lys, etc) MASS 40 NS 14.01 ! sp2 N; note N* --> NS to avoid confusion with wildcard MASS 41 O 16.00 ! carbonyl group oxygen MASS 42 OW 16.00 ! oxygen in TIP3P water MASS 43 OH 16.00 ! oxygen in hydroxyl group MASS 44 OS 16.00 ! ether and ester oxygen MASS 45 O2 16.00 ! carboxyl and phosphate group oxygen MASS 46 P 30.97 ! phosphate MASS 47 S 32.06 ! sulphur in disulfide linkage MASS 48 SH 32.06 ! sulphur in cystine MASS 49 CU 63.55 ! copper MASS 50 FE 55.00 ! iron MASS 51 Li 6.94 ! lithium MASS 52 K 39.10 ! potassium MASS 53 Rb 85.47 ! rubidium DECL -CA ! proteins DECL -C DECL -O DECL +N DECL +H DECL +CA DECL +P ! nucleic acids DECL +O1P DECL +O2P DECL +O5' DECL -O3' DEFAULT FIRST NTER LAST CTER AUTOGENERATE ANGLES DIHEDRAL RESIDUE ADE -1.0 ! note: this is RNA (RA); patches to make GROUP ! terminal or deoxyribose are required ATOM P P 1.1662 ATOM O1P O2 -0.7760 ATOM O2P O2 -0.7760 ATOM O5' OS -0.4989 ATOM C5' CT 0.0558 ATOM H5' H1 0.0679 ! note: type is H5'1 --> this should be checked ATOM H5'' H1 0.0679 ! note: type is H5'2 ATOM C4' CT 0.1065 ATOM H4' H1 0.1174 ATOM O4' OS -0.3548 ATOM C1' CT 0.0394 ATOM H1' H2 0.2007 ATOM N9 NS -0.0251 ! note: type is N* ATOM C8 CK 0.2006 ATOM H8 H5 0.1553 ATOM N7 NB -0.6073 ATOM C5 CB 0.0515 ATOM C6 CA 0.7009 ATOM N6 N2 -0.9019 ATOM H61 H 0.4115 ATOM H62 H 0.4115 ATOM N1 NC -0.7615 ATOM C2 CQ 0.5875 ATOM H2 H5 0.0473 ATOM N3 NC -0.6997 ATOM C4 CB 0.3053 ATOM C3' CT 0.2022 ATOM H3' H1 0.0615 ATOM C2' CT 0.0670 ATOM H2'' H1 0.0972 ! note: this is H2'1 ATOM O2' OH -0.6139 ATOM H2' HO 0.4186 ! note: this is HO'2 ATOM O3' OS -0.5246 ! using charmm bond lists (top_all22_na.inp) BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 N7 C8 BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 IMPROPER C8 C4 N9 C1' IMPROPER C6 H61 N6 H62 IMPROPER N7 N9 C8 H8 IMPROPER N1 N3 C2 H2 IMPROPER C5 N1 C6 N6 DONO H61 N6 DONO H62 N6 DONO H2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' ! using charmm geometry (top_all22_na.inp) IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATCH FIRST ADE5 LAST ADE3 RESIDUE URA -1.0 ! note: this is RNA (RA); patches to make GROUP ! terminal are required. ATOM P P 1.1662 ATOM O1P O2 -0.7760 ATOM O2P O2 -0.7760 ATOM O5' OS -0.4989 ATOM C5' CT 0.0558 ATOM H5' H1 0.0679 ! note: name is H5'1 ATOM H5'' H1 0.0679 ! note: name is H5'2 ATOM C4' CT 0.1065 ATOM H4' H1 0.1174 ATOM O4' OS -0.3548 ATOM C1' CT 0.0674 ATOM H1' H2 0.1824 ATOM N1 NS 0.0418 ! note: type is N* ATOM C6 CM -0.1126 ATOM H6 H4 0.2188 ATOM C5 CM -0.3635 ATOM H5 HA 0.1811 ATOM C4 C 0.5952 ATOM O4 O -0.5761 ATOM N3 NA -0.3549 ATOM H3 H 0.3154 ATOM C2 C 0.4687 ATOM O2 O -0.5477 ATOM C3' CT 0.2022 ATOM H3' H1 0.0615 ATOM C2' CT 0.0670 ATOM H2'' H1 0.0972 ! note: name is H2'1 ATOM O2' OH -0.6139 ATOM H2' HO 0.4186 ! note: name is HO'2 ATOM O3' OS -0.5246 ! bonds from charmm (top_all22_na.inp) BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 BOND C5 C6 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 IMPROPER C6 C2 N1 C1' IMPROPER C4 C6 C5 H5 IMPROPER N1 N3 C2 O2 IMPROPER C5 N3 C4 O4 IMPROPER C2 C4 N3 H3 IMPROPER N1 C5 C6 H6 DONO H3 N3 DONO H2' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' ! build from charmm (top_all22_na.inp) IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 IC C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATCH FIRST URA5 LAST URA3 RESIDUE THY -1.0 ! note: this is DNA (DT); patches to make GROUP ! terminal are required ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0680 ATOM H1' H2 0.1804 ATOM N1 NS -0.0239 ! this is atom type N* ATOM C6 CM -0.2209 ATOM H6 H4 0.2607 ATOM C5 CM 0.0025 ATOM C7 CT -0.2269 ATOM H71 HC 0.0770 ATOM H72 HC 0.0770 ATOM H73 HC 0.0770 ATOM C4 C 0.5194 ATOM O4 O -0.5563 ATOM N3 NA -0.4340 ATOM H3 H 0.3420 ATOM C2 C 0.5677 ATOM O2 O -0.5881 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2' HC 0.0718 ! this is H2'1 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM O3' OS -0.5232 ! bonds from charmm (top_all22_na.inp) ! swapped C5M with C7 ! swapped H5? with H7? BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 BOND C5 C7 C5 C6 C2' C3' C3' O3' O3' +P BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C6 H6 C7 H71 C7 H72 C7 H73 BOND C2' H2' IMPROPER C6 C2 N1 C1' IMPROPER C4 C6 C5 C7 IMPROPER N1 N3 C2 O2 IMPROPER C5 N3 C4 O4 IMPROPER C2 C4 N3 H3 IMPROPER N1 C5 C6 H6 DONO H3 N3 ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O3' ACCE O4' ACCE O5' ! build from charmm (top_all22_na.inp) ! name swapping as above, delete references to O2' IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C7 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C7 H71 0.0 0.0 0.0 0.0 0.0 IC C5 H71 *C7 H72 0.0 0.0 115.0 0.0 0.0 IC H71 H72 *C7 H73 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATCH FIRST THY5 LAST THY3 RESI CYT -1.0 ! note: this is RNA (RC); patches to make GROUP ! terminal or deoxyribose are required ATOM P P 1.1662 ATOM O1P O2 -0.7760 ATOM O2P O2 -0.7760 ATOM O5' OS -0.4989 ATOM C5' CT 0.0558 ATOM H5' H1 0.0679 ! this is H5'1 ATOM H5'' H1 0.0679 ! this is H5'2 ATOM C4' CT 0.1065 ATOM H4' H1 0.1174 ATOM O4' OS -0.3548 ATOM C1' CT 0.0066 ATOM H1' H2 0.2029 ATOM N1 NS -0.0484 ! this is type N* ATOM C6 CM 0.0053 ATOM H6 H4 0.1958 ATOM C5 CM -0.5215 ATOM H5 HA 0.1928 ATOM C4 CA 0.8185 ATOM N4 N2 -0.9530 ATOM H41 H 0.4234 ATOM H42 H 0.4234 ATOM N3 NC -0.7584 ATOM C2 C 0.7538 ATOM O2 O -0.6252 ATOM C3' CT 0.2022 ATOM H3' H1 0.0615 ATOM C2' CT 0.0670 ATOM H2'' H1 0.0972 ! this is H2'1 ATOM O2' OH -0.6139 ATOM H2' HO 0.4186 ! this is HO'2 ATOM O3' OS -0.5246 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 BOND C4 C5 C5 C6 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 IMPROPER C6 C2 N1 C1' IMPROPER N1 N3 C2 O2 IMPROPER C4 H41 N4 H42 IMPROPER N1 C5 C6 H6 IMPROPER C6 C4 C5 H5 IMPROPER N3 C5 C4 N4 DONO H42 N4 DONO H2' O2' DONO H41 N4 ACCE O2 C2 ACCE N3 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.79 1.399 IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATCH FIRST CYT5 LAST CYT3 RESI GUA -1.0 ! note: this is GUA (RG); patches to make GROUP ! terminal or deoxyribose are required ATOM P P 1.1662 ATOM O1P O2 -0.7760 ATOM O2P O2 -0.7760 ATOM O5' OS -0.4989 ATOM C5' CT 0.0558 ATOM H5' H1 0.0679 ! this is H5'1 ATOM H5'' H1 0.0679 ! this is H5'2 ATOM C4' CT 0.1065 ATOM H4' H1 0.1174 ATOM O4' OS -0.3548 ATOM C1' CT 0.0191 ATOM H1' H2 0.2006 ATOM N9 NS 0.0492 ! this is type N* ATOM C8 CK 0.1374 ATOM H8 H5 0.1640 ATOM N7 NB -0.5709 ATOM C5 CB 0.1744 ATOM C6 C 0.4770 ATOM O6 O -0.5597 ATOM N1 NA -0.4787 ATOM H1 H 0.3424 ATOM C2 CA 0.7657 ATOM N2 N2 -0.9672 ATOM H21 H 0.4364 ATOM H22 H 0.4364 ATOM N3 NC -0.6323 ATOM C4 CB 0.1222 ATOM C3' CT 0.2022 ATOM H3' H1 0.0615 ATOM C2' CT 0.0670 ATOM H2'' H1 0.0972 ! this is H2'1 ATOM O2' OH -0.6139 ATOM H2' HO 0.4186 ! this is HO'2 ATOM O3' OS -0.5246 ! bonds from charmm (top_all22_na.inp) BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 BOND C5 N7 N7 C8 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 IMPROPER C8 C4 N9 C1' IMPROPER C5 N1 C6 O6 IMPROPER C6 C2 N1 H1 IMPROPER C2 H21 N2 H22 IMPROPER N7 N9 C8 H8 IMPROPER N1 N3 C2 N2 DONO H21 N2 DONO H22 N2 DONO H1 N1 DONO H2' O2' ACCE O6 C6 ACCE N3 ACCE N7 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' ! build array from charmm (top_all22_na.inp) IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -96.0 125.59 1.3783 IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATCH FIRST GUA5 LAST GUA3 RESI WAT 0.00 ! TIPS3P WATER MODEL ! GENERATE USING NOANGLE NODIHEDRAL GROUP ATOM OH2 OW -0.834 ATOM H1 HW 0.417 ATOM H2 HW 0.417 BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE ANGLE H1 OH2 H2 ! REQUIRED PATCHING FIRS NONE LAST NONE RESI CIP 1.00 ! Sodium Ion GROUP ATOM NA IP 1.00 PATCHING FIRST NONE LAST NONE ! ! Definition of patch residues ! ! ! 5'-terminal adenine, replace phosphate by hydroxyl ! PRES ADE5 -0.1928 ATOM H5T HO 0.4295 ATOM O5' OH -0.6223 DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P BOND H5T O5' IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 ! ! 5'-terminal uracil, replace phosphate by hydroxyl ! PRES URA5 -0.1928 ATOM H5T HO 0.4295 ATOM O5' OH -0.6223 DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P BOND H5T O5' DONO H5T O5' IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 ! ! 5'-terminal thymine, replace phosphate by hydroxyl ! PRES THY5 -0.1896 ATOM H5T HO 0.4422 ATOM O5' OH -0.6318 DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P BOND H5T O5' DONO H5T O5' IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 ! ! 5'-terminal cytosine, replace phosphate by hydroxyl ! PRES CYT5 -0.1928 ATOM H5T HO 0.4295 ATOM O5' OH -0.6223 DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P BOND H5T O5' DONO H5T O5' IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 ! ! 5'-terminal guanine, replace phosphate by hydroxyl ! PRES GUA5 -0.1928 ATOM H5T HO 0.4295 ATOM O5' OH -0.6223 DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P BOND H5T O5' DONO H5T O5' IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 ! ! 3'-terminal adenine, add terminal hydrogen ! PRES ADE3 -0.2165 ATOM O3' OH -0.6541 ATOM H3T HO 0.4376 BOND O3' H3T DONO H3T O3' IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 ! ! 3'-terminal uracil, add terminal hydrogen ! PRES URA3 -0.2165 ATOM O3' OH -0.6541 ATOM H3T HO 0.4376 BOND O3' H3T DONO H3T O3' IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 ! ! 3'-terminal thymine, add terminal hydrogen ! PRES THY3 -0.2153 ATOM O3' OH -0.6549 ATOM H3T HO 0.4396 BOND O3' H3T DONO H3T O3' IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 ! ! 3'-terminal cytosine, add terminal hydrogen ! PRES CYT3 -0.2165 ATOM O3' OH -0.6541 ATOM H3T HO 0.4376 BOND O3' H3T DONO H3T O3' IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 ! ! 3'-terminal guanine, add terminal hydrogen ! PRES GUA3 -0.2165 ATOM O3' OH -0.6541 ATOM H3T HO 0.4376 BOND O3' H3T DONO H3T O3' IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 ! ! DEOXYRIBOSE PATCHES, NOTE: these are made extra tricky by the fact ! that all the charges change upon conversion from RNA to DNA and ! some atom types change as well. This requires special patches for ! 5'-terminal, standard and 3'-terminal residues. ! ! ! deoxyribose patch for adenine 5'-terminal ! PRES DOA5 -0.3079 DELETE ATOM O2' ATOM H5T HO 0.4422 ATOM O5' OH -0.6318 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! note: type is H5'1 --> this should be checked ATOM H5'' H1 0.0754 ! note: type is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0431 ATOM H1' H2 0.1838 ATOM N9 NS -0.0268 ! note: type is N* ATOM C8 CK 0.1607 ATOM H8 H5 0.1877 ATOM N7 NB -0.6175 ATOM C5 CB 0.0725 ATOM C6 CA 0.6897 ATOM N6 N2 -0.9123 ATOM H61 H 0.4167 ATOM H62 H 0.4167 ATOM N1 NC -0.7624 ATOM C2 CQ 0.5716 ATOM H2 H5 0.0598 ATOM N3 NC -0.7417 ATOM C4 CB 0.3800 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! note: this is H2'2 ATOM H2' HC 0.0718 ! note: this is H2'1 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for adenine ! PRES DOA -1.0 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! note: type is H5'1 --> this should be checked ATOM H5'' H1 0.0754 ! note: type is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0431 ATOM H1' H2 0.1838 ATOM N9 NS -0.0268 ! note: type is N* ATOM C8 CK 0.1607 ATOM H8 H5 0.1877 ATOM N7 NB -0.6175 ATOM C5 CB 0.0725 ATOM C6 CA 0.6897 ATOM N6 N2 -0.9123 ATOM H61 H 0.4167 ATOM H62 H 0.4167 ATOM N1 NC -0.7624 ATOM C2 CQ 0.5716 ATOM H2 H5 0.0598 ATOM N3 NC -0.7417 ATOM C4 CB 0.3800 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2' HC 0.0718 ! note: this is H2'1 ATOM H2'' HC 0.0718 ! note: this is H2'2 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for 3'-terminal adenine ! PRES DOA3 -0.6921 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! note: type is H5'1 --> this should be checked ATOM H5'' H1 0.0754 ! note: type is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0431 ATOM H1' H2 0.1838 ATOM N9 NS -0.0268 ! note: type is N* ATOM C8 CK 0.1607 ATOM H8 H5 0.1877 ATOM N7 NB -0.6175 ATOM C5 CB 0.0725 ATOM C6 CA 0.6897 ATOM N6 N2 -0.9123 ATOM H61 H 0.4167 ATOM H62 H 0.4167 ATOM N1 NC -0.7624 ATOM C2 CQ 0.5716 ATOM H2 H5 0.0598 ATOM N3 NC -0.7417 ATOM C4 CB 0.3800 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2' HC 0.0718 ! note: this is H2'1 ATOM H2'' HC 0.0718 ! note: this is H2'2 ATOM O3' OH -0.6549 ATOM H3T HO 0.4396 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for 5'-terminal cytosine ! PRES DOC5 -0.3079 DELETE ATOM O2' ATOM H5T HO 0.4422 ATOM O5' OH -0.6318 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT -0.0116 ATOM H1' H2 0.1963 ATOM N1 NS -0.0339 ! this is type N* ATOM C6 CM -0.0183 ATOM H6 H4 0.2293 ATOM C5 CM -0.5222 ATOM H5 HA 0.1863 ATOM C4 CA 0.8439 ATOM N4 N2 -0.9773 ATOM H41 H 0.4314 ATOM H42 H 0.4314 ATOM N3 NC -0.7748 ATOM C2 C 0.7959 ATOM O2 O -0.6548 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'1 ATOM H2' HC 0.0718 ! this is HO'2 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for cytosine ! PRES DOC -1.00 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT -0.0116 ATOM H1' H2 0.1963 ATOM N1 NS -0.0339 ! this is type N* ATOM C6 CM -0.0183 ATOM H6 H4 0.2293 ATOM C5 CM -0.5222 ATOM H5 HA 0.1863 ATOM C4 CA 0.8439 ATOM N4 N2 -0.9773 ATOM H41 H 0.4314 ATOM H42 H 0.4314 ATOM N3 NC -0.7748 ATOM C2 C 0.7959 ATOM O2 O -0.6548 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM H2' HC 0.0718 ! this is H2'1 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for 3'-terminal cytosine ! PRES DOC3 -0.6921 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT -0.0116 ATOM H1' H2 0.1963 ATOM N1 NS -0.0339 ! this is type N* ATOM C6 CM -0.0183 ATOM H6 H4 0.2293 ATOM C5 CM -0.5222 ATOM H5 HA 0.1863 ATOM C4 CA 0.8439 ATOM N4 N2 -0.9773 ATOM H41 H 0.4314 ATOM H42 H 0.4314 ATOM N3 NC -0.7748 ATOM C2 C 0.7959 ATOM O2 O -0.6548 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM H2' HC 0.0718 ! this is H2'1 ATOM O3' OH -0.6549 ATOM H3T HO 0.4396 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for 5'-terminal guanine ! PRES DOG5 -0.3079 DELETE ATOM O2' ATOM H5T HO 0.4422 ATOM O5' OH -0.6318 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0358 ATOM H1' H2 0.1746 ATOM N9 NS 0.0577 ! this is type N* ATOM C8 CK 0.0736 ATOM H8 H5 0.1997 ATOM N7 NB -0.5725 ATOM C5 CB 0.1991 ATOM C6 C 0.4918 ATOM O6 O -0.5699 ATOM N1 NA -0.5053 ATOM H1 H 0.3520 ATOM C2 CA 0.7432 ATOM N2 N2 -0.9230 ATOM H21 H 0.4235 ATOM H22 H 0.4235 ATOM N3 NC -0.6636 ATOM C4 CB 0.1814 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM H2' HC 0.0718 ! this is H2'1 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for guanine ! PRES DOG -1.00 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0358 ATOM H1' H2 0.1746 ATOM N9 NS 0.0577 ! this is type N* ATOM C8 CK 0.0736 ATOM H8 H5 0.1997 ATOM N7 NB -0.5725 ATOM C5 CB 0.1991 ATOM C6 C 0.4918 ATOM O6 O -0.5699 ATOM N1 NA -0.5053 ATOM H1 H 0.3520 ATOM C2 CA 0.7432 ATOM N2 N2 -0.9230 ATOM H21 H 0.4235 ATOM H22 H 0.4235 ATOM N3 NC -0.6636 ATOM C4 CB 0.1814 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM H2' HC 0.0718 ! this is H2'1 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for 3'-terminal guanine ! PRES DOG3 -0.6921 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0358 ATOM H1' H2 0.1746 ATOM N9 NS 0.0577 ! this is type N* ATOM C8 CK 0.0736 ATOM H8 H5 0.1997 ATOM N7 NB -0.5725 ATOM C5 CB 0.1991 ATOM C6 C 0.4918 ATOM O6 O -0.5699 ATOM N1 NA -0.5053 ATOM H1 H 0.3520 ATOM C2 CA 0.7432 ATOM N2 N2 -0.9230 ATOM H21 H 0.4235 ATOM H22 H 0.4235 ATOM N3 NC -0.6636 ATOM C4 CB 0.1814 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM H2' HC 0.0718 ! this is H2'1 ATOM O3' OH -0.6549 ATOM H3T HO 0.4396 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 END