[gmx-users] Multiprotein lipid bilayer

[ram bio]

hi justin,

will try that ....

thanks

Ram

On Thu, Mar 4, 2010 at 4:51 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 <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
>>>> 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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