[gmx-users] POPC: ff53a6 and CHARMM36 formats

[Anirban Ghosh]

Thanks Angel and Justin.
Will try out the options!

Regards,

-Anirban

On Tue, May 1, 2012 at 5:46 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/1/12 8:05 AM, Ángel Piñeiro wrote:
>
>> I guess there are better solutions but an alternative is to map your
>> bilayer to
>> MARTINI (http://md.chem.rug.nl/**cgmartini/<http://md.chem.rug.nl/cgmartini/>)
>> and then to use SUGAR-PIE
>> (http://smmb.usc.es/sugarpie/**sugarpie.php<http://smmb.usc.es/sugarpie/sugarpie.php>)
>> to go to from MARTINI to all-atom
>> CHARMM36.
>>
>>
> Even simpler would be to fix the offending atom names and build a suitable
> .hdb entry (if one does not already exist) and produce the topology with
> pdb2gmx.  I would think it would then be far easier to preserve the
> original configurations of the lipids, rather than changing the resolution
> back and forth.
>
> -Justin
>
>  Hope it helps,
>>
>> Ángel.
>>
>>
>> On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote:
>>
>>> Hi ALL,
>>>
>>>
>>> I have a equilibrated POPC bilayer (100 ns run) that I have run using
>>> GROMOS
>>> ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation
>>> using
>>> CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming
>>> conventions
>>> (N, P, C, O) between this two FFs as a result of which pdb2gmx gives
>>> error.
>>> Can these atom names (hydrogens can be ignored) of my equilibrated POPC
>>> bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot
>>> in
>>> advance.
>>>
>>>
>>>
>>>
>>> Regards,
>>>
>>>
>>> Anirban
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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