Thank you for responce and explanation! So is it a good alghorithm to use gromacs genrestr command and then include this posre.itp file into topology (without any changes) after insertion of a ligand.itp?
Thank you in advance On 4/2/13 6:07 AM, alex rayevsky wrote: Dear All! I have a doubt about the rightness of ligand/molecule integration in the topology file. I'm using an amber (tleap) or swissparam.ch to build a topology of the residue (modified trna). Is it neccessary to generate a position restrain file (genrestr program) for this residue or not? I've started both dynamics with/without posrestraints on my residue, however I'm really not sure that my results from both of them are different. But I want to do everything in right way, so what can you say about this? Restraints during equilibration are used to prevent unnatural forces from theunequilibrated solvent and help prevent deformation of the structure. It's never a bad idea to restrain the whole solute. If I were reading a paper thatdescribed restraining the whole solute, except for one residue because it wasspecial or difficult to deal with, I would immediately be suspicious. -Justin -- **** * Nemo me impune lacessit* -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
