[gmx-users] specbond files

[Justin Lemkul]

On 6/16/15 7:02 AM, faride badalkhani wrote:
> Dear all,
>
> I need to use specbond.dat file for a branched polymer, but I do not know
> what is the meaning of: the new name for residue A and the new name for
> residue B!
> Could you help me with this?
>

Changes in bonded state typically require modification of residue definition 
(atoms added or deleted, changes in atom type, etc), so new names refer to new 
.rtp entries. See existing examples in the .rtp.

-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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