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?
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
There is also a membrane protein tutorial linked from
http://www.gromacs.org/Documentation/Tutorials
The approach is slightly different from what has been posted before, but perhaps
it will be of some use.
-Justin
Bests
2011/9/22 lina <[email protected] <mailto:[email protected]>>
On Thu, Sep 22, 2011 at 11:34 AM, elisa carli
<[email protected] <mailto:[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
<https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB>
mdrun_g -v -deffnm em
works well.
--
Best Regards,
lina
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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