[gmx-users] CHARMM27 hates my DMPC

Vytautas Rakeviius vytautas1987 at yahoo.com
Tue Apr 4 15:39:16 CEST 2017

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441



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