ptraj/rdparm is a program written in C that has two functions.
- rdparm reads in AMBER prmtop files and allows users to inspect the stored information (see rdparm.html).
- ptraj is a program for processing AMBER, CHARMM, and PDB trajectory files. It can convert trajectories, calculate bond, angles, dihedrals, RMSd value, mean-squared displacements, atomic positional fluctuations, order parameters/correlation functions, imaging of trajectories to various unit cells, etc..
Please let us know if you find bugs or add features of general use...
- Cornell et al. force field within CHARMM.
cornell_all.rtf (residue/topology file)
cornell_na.rtf (residue/topology file for nucleic acids)
cornell_na.prm (parameters for nucleic acids only)
- The parm98.dat nucleic acid force field in AMBER. This improves
sugar pucker phases and glycosidic torsion (chi) values for B-DNA in
Cornell et al. (at the expense of A-DNA stabilization in mixed
water/ethanol solutions and B-DNA to A-DNA transitions with