[gmx-users] pdb2gmx fails on CHARMM36 terminal group

[Justin Lemkul]

On 3/13/17 1:48 PM, Davit Hakobyan wrote:
> Just a small note about cholesterol CHL1 in the merged.rtp file of november 2016
> release for CHARMM36 force field.
> The first four lines of CHL1 in merged.rtp:
>        C3  CRL1    0.140  0
>        O3   OHL   -0.660  1
>       H3'   HOL    0.430  2
>        H3  HGA1    0.090  3
>
> While the sequence should be:
>        C3  CRL1    0.140  0
>        H3  HGA1    0.090  3
>        O3   OHL   -0.660  1
>       H3'   HOL    0.430  2
>
> So that each hydrogen atom follow immediately the heavy atom. One could have
> this in mind for the next release?

I'll fix it in the next release.  We read the residue definitions directly from 
CHARMM force field files, which for some reason had the weird atom order.  There 
should be no functional consequence, though.  It will be in the intuitive order 
when we release a new version of the port (which will probably be soon since 
people have asked for a few things to be converted recently).

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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