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[Justin Lemkul]

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On 11/12/19 5:29 AM, shakuntala dhurua wrote:
> hello,
> Here I want to generate arg.pdb to arg.gro by using amber99sb force field .
> for test i have used 1 residue of arginine but i got Fatal error:
> There is a dangling bond at at least one of the terminal ends and the force
> field does not provide terminal entries or files. Fix your terminal
> residues so that they match the residue database (.rtp) entries, or provide
> terminal database entries (.tdb). and following is the attach pdb format
> which i have used for pdb2gmx ,please suggest me to solve this problem

AMBER does not support zwitterionic forms of single amino acids, at 
least not within GROMACS. There may be a way to create such residues 
from the AMBER parameter database, but you'll have to look into 
published works on their force field parametrization to see if such 
residue definitions exist.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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