[gmx-users] Multiprotein lipid bilayer
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 4 16:51:18 CET 2010
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:
in your .top file.
Other ways to insert proteins might include using genbox creatively, VMD,
g_membed, etc. Search the list archive.
> On Thu, Mar 4, 2010 at 4:36 PM, Justin A. Lemkul <jalemkul at 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
>> 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:
>>> Thanks in advance,
>> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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