Hi Lisa Thank you very much for your reply. After minimimization could I run a molecular dynamic production? Or have I to do other sets? Could you write me which are the commands to execute up to MD run?
Bests 2011/9/22 lina <[email protected]> > On Thu, Sep 22, 2011 at 11:34 AM, elisa carli <[email protected]>wrote: > >> Dear All >> >> I'd like to perfom a MD simulation on a membrane protein using DLPC or >> DPPC system >> I've downloaded the API package from this link >> http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies >> >> DPPC.zip and DLPC.zip by schiu >> >> How can I use them? Where can I get a tutorial or commands illustrating >> the use of these packages? >> >> Thanks in advance >> > Here is a rough procedure: > > http://www.nanoconductor.org/43A1-S3/ > > Took Chiu's DPPC.zip as an example. We use the speptide.pdb peptide from > the gromacs tutorial (it's a bad choice to put it in the dppc, but we just > try it). > > pdb2gmx_g -f speptide.pdb -o speptide.gro > > choose > 9: GROMOS96 43a1 force field > 1: SPC simple point charge, recommended > > $ tail -1 dppc.gro > 5.68585 5.60685 6.85739 > > To be as simple as possible here, we use the dimension of the dppc.gro > > editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5 4.2 > -box 5.68585 5.60685 6.85739 > > now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by > > genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top > > > Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide, > > the purpose of doing a simple energy minimization here just want to "test" > the topol.top. > > it used 43A1-S3 force field (You can download from > http://www.nanoconductor.org/43A1-S3/). > > The head of topol.top: > ; Include forcefield parameters > #include "ffG43A1-S3.itp" > #include "lipids_43A1-S3.itp" > > The tail of topol.top: > > [ molecules ] > ; Compound #mols > Protein 1 > DPPC 71 > SOL 3205 > > I manually added DPPC 71. > > please copy the lipids_43A1-S3.itp ffG43A1-S3.itp > ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into current > directory, > extra copy ff_dum.itp from > some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current working > directory. > > I attached all those files in try.tar.gz > > https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB > > mdrun_g -v -deffnm em > > works well. > > > -- > Best Regards, > > lina > > > > -- > 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 >
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