Hi everybody, I want do to an energy minimization and simulation with position restraints. Additionally to the protein I have a membrane around my protein which I also ant to fix. If I won't fix it, it is in the whole box after the minimization and simulation but not around my protein. Since I only want the hydrogen atoms to be flexible I use the second option "protein-h" when I was asked by genrestr. This makes that the whole protein including the membrane of dummy atoms is fix. But when I want to use grompp I get the error:
Atom index (4942) in position_restraints out of bounds (1-4941). 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. The first 4941 atoms are of the "real" protein without the membrane and after this the membrane starts: 313LEU OC1 4940 3.429 4.330 3.090 313LEU OC2 4941 3.337 4.305 3.259 314DUM DUM 4942 1.996 2.371 6.171 315DUM DUM 4943 1.996 2.371 6.271 316DUM DUM 4944 1.996 2.471 6.171 When I remove the restriction of the DUM atoms I don't get the error but that is not what I want. Can you please tell me how I can fix the membrane? Thank you, Eva -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
