ram bio wrote:
HI Justin,
Thanks for the info.
I have followed your tutorial earlier, it really works, and that was
for 1 protein, but if 2 or more different kinds of proteins are to be
inserted then how to generate the a single topology file for all the
proteins using pdb2gmx and also can you please let me know the other
ways to insert the proteins in lipid bilayers....
You don't need a single topology for all the proteins. Instead you can generate
individual topologies for each protein with pdb2gmx, remove the unnecessary
#includes, [system], and [molecules] directives to make them single-molecule
.itp files, and then simply:
#include "protein_A.itp"
#include "protein_B.itp"
in your .top file.
Other ways to insert proteins might include using genbox creatively, VMD,
g_membed, etc. Search the list archive.
-Justin
Ram
On Thu, Mar 4, 2010 at 4:36 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
ram bio wrote:
Dear Gromacs Users,
I would like to run molecular dynamics by inserting multiple proteins
in the same lipid bilayer using gromacs, is it possible? if so, please
Just about anything is possible :)
let me know if any tutorial is available or any kind of help is
available....
There is a tutorial for a basic membrane protein system linked from the
Gromacs tutorials page. As for inserting multiple proteins in the membrane,
there are several ways to do it, but if you want to use InflateGRO, you'll
need the latest version:
http://www.csb.bit.uni-bonn.de/inflategro.html
-Justin
Thanks in advance,
Ram
--
========================================
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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--
========================================
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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