[gmx-users] MD with membrane protein
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 3 20:59:16 CEST 2011
elisa carli wrote:
> 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?
There is also a membrane protein tutorial linked from
The approach is slightly different from what has been posted before, but perhaps
it will be of some use.
> 2011/9/22 lina <lina.lastname at gmail.com <mailto:lina.lastname at gmail.com>>
> On Thu, Sep 22, 2011 at 11:34 AM, elisa carli
> <elisacarli21 at gmail.com <mailto:elisacarli21 at 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
> 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:
> 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
> 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
> 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
> mdrun_g -v -deffnm em
> works well.
> Best Regards,
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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