[gmx-users] POPC: ff53a6 and CHARMM36 formats

Justin A. Lemkul jalemkul at vt.edu
Tue May 1 14:16:14 CEST 2012

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/) and then to use SUGAR-PIE
> (http://smmb.usc.es/sugarpie/sugarpie.php) 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,
> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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