[gmx-users] Termini database-more details , meaning of each lines and how to add or delete atoms-reg

[Justin Lemkul]

On 8/15/15 1:32 PM, Nikhil Maroli wrote:
> how to add and  delete atoms  and meaning of each lines in both
> aminoacids.n.tdb and aminoacid.c.tdb
>

Read the manual, section 5.6.5 where everything is explained.

> My structure is cyclic peptide rings i have to remove  Oxygen from -COO end
> Hydrogen from -NH3 end  of the first and last amino acids..
>

This doesn't require .tdb modification.  Choose 'None' for the termini and 
either use specbond.dat to complete the cyclization or manually add the bonded 
interactions yourself.

-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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