[gmx-users] POPC: ff53a6 and CHARMM36 formats
reach.anirban.ghosh at gmail.com
Wed May 2 06:24:47 CEST 2012
Thanks Angel and Justin.
Will try out the options!
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
>> to go to from MARTINI to all-atom
> 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.
> Hope it helps,
>> 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
>>> ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation
>>> CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming
>>> (N, P, C, O) between this two FFs as a result of which pdb2gmx gives
>>> 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
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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
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