Hello, I am trying to generate a topology file for my protein which has three disulfide bonds using ffG53a5. I realized in the topology file that the force field parameters for bonds, angle and dihedrals of my S-S bonds are missing. I found the following thread about this issue:
http://lists.gromacs.org/pipermail/gmx-users/2011-November/066371.html Using version 4.5.4, I typed grompp -p topol.top -pp topol-processed.top -f systemem.mdp -c protein-solvated-neutral.gro to generate the processed topology file. These terms are still missing in the processed topology file, but grompp complained nothing. Am I safe? Is there still sth going on that takes care of the missing terms in the topology file? Thanks for your help. Best, Paymon -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
