[gmx-users] CHARMM27 hates my DMPC

[Vytautas Rakeviius]

Thanks, I reused DMPC layers from CHARMM-GUI after some editing.I was able to pin-down issue here, test file:http://www.mediafire.com/file/usuv55c3j505ec2/test.pdbI can do:gmx pdb2gmx -f test.pdb -o test.gro -water spce
Without error. But if I do:gmx pdb2gmx -f test.pdb -o test.gro -water spce -ignhI get error about hydrogen which I try to ignore. Very strange for me. -ignh option is not possible with CHARMM ff?


 

    On Tuesday, April 4, 2017 3:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 

 

On 4/4/17 8:52 AM, Vytautas Rakeviius wrote:
> Hello,
> I have my system with DMPC bilayers in pdb and try to convert it into GROMACS input. Because system is with lipids I think chose CHARMM27 ff. But still I get lots of warnings like that:
>
> https://pastebin.com/K8dHKkUi
> Also I add my DMPC pdb as example. What should I do? Rename all my DMPC atoms?Thanks for all suggestions.
>
>

This is the same with any force field; the atom names have to match the force 
field's expectations.

If you're just trying to build a DMPC bilayer, construct one using CHARMM-GUI. 
It's guaranteed to have CHARMM-compliant nomenclature (and you should be using 
CHARMM36 for lipids, anyway, because the CHARMM27 parameters are not nearly as 
good for lipids).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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