[gmx-users] (no subject)

[shakuntala dhurua]

thanks Prof. Justin

On Tue, Nov 12, 2019 at 8:48 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
> Please use an appropriate subject line.
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
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