On Tue, Feb 15, 2011 at 5:25 PM, Parul tew <parul...@gmail.com> wrote:
> Hi all, > first I would like to thank Justin A. Lemkul for the tutorials provided which > are very helpful for new users like me. > I am doing a membrane protein simulation and now doing packing of the lipids > around the protein. I had run the inflategro.pl script and > > and now I am facing a problem doing energy minimization of my inflated system > (contatining protein and the lipid membrane) using grompp. > I have updated my topology file accordingly ie removed the spc.itp, ions.itp > it now only contains protein and dppc > > the protein is of 3881 atoms but after updating my topolgy it still gives the > following error: > Fatal error: > number of coordinates in coordinate file (system_inflated.gro, 9331) > does not match topology (topol.top, 10281) > > As i understand it could be because of the deleted lipids of the system, if > so how can I know the deleted number of lipids. > > My topology file looks like > ----------------------------------------------------------------------------------------------------------------------------- > > ; > ; This is your topology file > ; protein > ; > ; Include forcefield parameters > #include "ffG53a6_lipid.itp" > > [ moleculetype ] > ; Name nrexcl > Protein_A 3 > > [ atoms ] > . > . > . > . > ; Strong position restraints for InflateGRO > #ifdef STRONG_POSRES > #include "strong_posre.itp" > #endif > > ; Include DPPC chain topology > #include "dppc.itp" > > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > > [ system ] > ; Name > protein > 128-Lipid DPPC Bilayer > > [ molecules ] > ; Compound #mols > Protein_A 1 > DPPC 128 > > After insertion, there are probably several DPPC molecules removed. Check outputs from inflategro.pl, then update accordingly. Terry ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > thank you, > Parul Tewatia > > > > -- > 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 >
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