[gmx-users] (no subject)

shakuntala dhurua madhu.dhurua94 at gmail.com
Wed Nov 13 11:45:06 CET 2019


thanks Bratin for your suggestion

On Tue, 12 Nov 2019, 7:54 pm Bratin Kumar Das, <177cy500.bratin at nitk.edu.in>
wrote:

> I think you have capped your residue in the N-terminal and C-terminal
> end...and the capping is not defined in your .rtp entry.. that's why this
> error is coming
>
> On Tue 12 Nov, 2019, 3:58 PM shakuntala dhurua, <madhu.dhurua94 at gmail.com>
> 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
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