Hello everyone, I'm computing the free energy of binding between a DNA base and a carbon nanotube. I'm following the recipe given in Boresch et. al. J. Phys. Chem. B. 107, 2003 where the ligand (the base in my case) is restrained. The free energy of turning on the restraints is included in the overall binding free energy. These restraints include 1 distance, 2 angle, and 3 dihedral restraints.
Unfortunately, I'm having problems including the correct restraints in my topology file. First off, the form of the angle restraint in Gromacs involves 4 (2 pairs) atoms. The restraint in the Boresch paper assumes that the angle is between 3 atoms. Is there anyway to apply the correct restraint in Gromacs? Also, it doesn't seem like the [ angle_restraints ] or [ dihedral_restraints ] sections can be perturbed in a free energy calculation. For example, when I include two sets of restraint parameters (one for topology A and one for topology B) for, say, dihedral restraints, I get the following error: ------------------------------------------------------- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1180 Fatal error: Incorrect number of parameters - found 9, expected 5 or 5. ------------------------------------------------------- How do I perturb (i.e. turn on) these restraints over the course of a simulation? Thanks, Bob Johnson _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
