Dear All My protein complex has three chains A B C. I created three posre.itp for backbone and some side chain which is not on the interface for each of the chain. I put these in .top file as follows
; File 'complex.top' was generated ; By user: shahid (511) ; On host: coe.iitd.ac.in ; At date: Thu Feb 17 17:52:59 2011 ; ; This is your topology file ; "They Paint Their Faces So Differently From Ours" (Gogol Bordello) ; ; Include forcefield parameters #include "ffG43a1.itp" ; Include A-chain topologies #include "complex_A.itp" #include "complex_B.itp" #include "complex_C.itp" #ifdef POSRES #include "posreA.itp" #include "posreB.itp" #include "posreC.itp" #endif If I keep only one posreA.itp then grompp runs without error but if I use all three or two posre.itp it gives following error. Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 1275 Fatal error: [ file posreB.itp, line 118 ]: Atom index (968) in position_restraints out of bounds (1-966). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. I separated including topology and defining posres in three different parts but even then it gives error and grompp fails. In my posre.itp generated by genrestr I selected a group containing backbone and some side chains. My Idea is to keep the backbone as well as side chain of all the residues which are not on interface fixed and allow free movement of only interface residue and then run full MD. For above procedure I defined define = POSRES in full.mdp Please suggest what should I do . For a single chain I did MD keeping backbone fixed and allowing side chain free movement. In my posres.itp I used a force of 2000 kj to keep them in fixed position with option genrestr -fc. Waiting for reply Shahid Nayeem -- 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
