[gmx-users] REGARDING DOUBT

[Justin Lemkul]

On 11/23/12 7:41 AM, Subramaniam Boopathi wrote:
> dear sir,
>           i have give input that is* ./pdb2gmx_d -f activesite16-22.pdb
> -water tip3p -ignh*
> but i face some* errror like There is a dangling bond at at least one of
> the terminal ends and the force field does not provide terminal entries or
> files. Edit a .n.tdb and/or .c.tdb fi*le. i have made necessary correction
> in the .rtp file acccording to my pdb file.
>

What changes did you make?  Do you have any unnatural amino acids or capping 
groups?  What are your terminal residues?  What force field are you using?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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