[gmx-users] pdb file for united atom force fields

Justin Lemkul jalemkul at vt.edu
Wed Aug 12 13:34:04 CEST 2015



On 8/12/15 12:46 AM, faride badalkhani wrote:
> Dear Gromacs users,
>
> I need to work with a united atom FF, but I have defined all the Hydrogens
> in my pdb file. Does it cause any problem in MD procedure?
>

Well, the UA force field won't use (most of) the H, so they obviously need to be 
removed.  If this is a biomolecule, pdb2gmx -ignh takes care of this for you.

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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