[gmx-users] cgenff CTAB

[Justin Lemkul]

On 3/30/16 4:34 PM, xy21hb wrote:
> Dear Justin,
>
>
> I fixed the naming problem as you said. Many thanks for your help.
> However, the Br- ion in the original pdb does not appear in the converted structure.
> I wonder how I can introduce it to the CHARMM ff in gromacs by changing the ions.itp file.
>

You have to parametrize it first; CHARMM does not support Br- (hence why it was 
removed from your structure).  There are ion parameters in the literature that 
may be compatible, but I cannot vouch for them.

-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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