i have some structure that doesn't have any similar topology in charmm22 (protein) & charmm 27 (lipid) and i have tried several servers such as, cgenff & swiss param, but the .rtf file generated from this method gathering all of atom types in one group, why?
is there something that i might be missing?
meanwhile, i want to use this topology in order to detect groups and atoms for running free energy perturbation simulation (fep)...
what should i do?
if someone who know the solution, i must to tell please guide me, i appreciate.
Have you tried antechamber which is a part of AmberTools. If not please follow the link for the program and tutorials,
Programs: http://ambermd.org/AmberTools.php
Tutorials: http://ambermd.org/antechamber/efz.html
Hope this will help.
Try PEPstrMOD PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues (http://osddlinux.osdd.net/raghava/pepstrmod/)
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