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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 CHARMM36.<BR>
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Hope it helps,<BR>
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Ángel.<BR>
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On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote:<BR>
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Hi ALL,
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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.
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Regards,
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Anirban
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