I've done all of that i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms )
I've included this in the topology of the bilayer ; Include chain topologies #include "gromos53a6_lipid.ff/forcefield.itp" #include "dppc.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" ; Include ion topologies #include "gromos53a6_lipid.ff/ions.itp" #ifdef POSRES_LIPID #include "posre_lipid.itp" #endif ; System specifications [ system ] 128-Lipid DMPC Bilayer in water [ molecules ] ; molecule name nr. DPPC 64 SOL 1193 SOL 690 Also I've tried to make posre for whole system ( large posres ) but it also was finished with same error Fatal error: [ file posre_lipid.itp, line 6 ]: Atom index (2) in position_restraints out of bounds (1-1). 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 What's most true for such multy system. Generate posre only for 1 part or for whole system? James 2011/10/31 Justin A. Lemkul <[email protected]> > > > James Starlight wrote: > >> Thanks, Justin >> I'll test your program soon. >> >> Today also I have some problems with generation of the posre for lipids >> >> I have lipid bilayer in pdb. Then I selected one lipid molecule and move >> it to separate pdb and convert it to gro via editconf. >> Than I've used genres and generate posre file for 1 lipid. Than I include >> tis posre to topology of my bilayer >> using gropt I obtain eror that I'm using wrong posre topology >> >> Also I've tried to include posre.itp to my lipid.itp ( this file contain >> link to posre on default) This run didnt produce any errors but as the >> result posres have not been worked ( I obtained perturbed bilayer after >> minimization) >> >> How I can generate work posre for my bilayer to prevent perturbation >> after equilibration or minimization ? >> >> > Since posre.itp is the default name given to the protein position > restraint file by pdb2gmx, the first step is to use a different name. > Then, you have to add the new #include statement in the correct location > in the topology. Presuming you do that, the lipids should be restrained in > whatever manner you've specified. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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