Hi. After successfully importing a CHARMM-generated PDB file to GROMACS I set out to do some short simulations. While all calculations finished without a problem if everything but the water molecules were fixed.
Removing the position restraints led to the system blowing up. Using J. Lemkul's tutorial suggestion I generated an index file selecting one lipid atom from sphingomyelin and one from cholesterol using make_ndx and the selection: a P | a O3 (alternatively I tried also "6 | 7 | 17 | 18 | a P | a O3"). Any of the two selections selects only atoms from the lipid part of the system. After creating the index file I used genrestr to position restrain the movements of the selected atoms and obtain a position restrain ITP file. I included this ITP file at the end of the lipid topology ITP file as instructed on GROMACS' website. In the last step I edited the MDP file to use the position restraints file for some lipid atoms but something went wrong as GROMPP complains: Fatal error: [ file sys9-tmp-ions-mini-nofix-2-posre.itp, line 116 ]: Atom index (12014) in position_restraints out of bounds (1-11954). 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. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Indeed, checking the lipid ITP file revealed there is no atom index 12014, yet there is an atom index 12014 (with the proper name) in the GRO file (that I used to create both the index and the restraints file) where all the atoms are listed. What have I done wrong? Thanks advance, Jernej Zidar -- 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
