On Thu, Sep 22, 2011 at 11:34 AM, elisa carli <elisacarl...@gmail.com>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
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