[gmx-users] MD with membrane protein

[lina]

On Thu, Sep 22, 2011 at 11:34 AM, elisa carli <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
> 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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