[gmx-users] Fatal error: atom C not found in buiding block 19NH2 while combining tdb and rtp

[Justin A. Lemkul]

On 5/23/12 1:26 PM, ankita oindrila wrote:
>   i am stimulting an AMP protein in water.
>
> this is the error i get on my first step..
>
> pdb2gmx -f 1PG1_1.pdb -o 1PG1_1_processed.gro -water spce
>
> error:
>
> Fatal error: atom C not found in buiding block 19NH2 while combining
> tdb and rtp
>
> please HELP!!

I suspect you're not selecting your termini correctly.  If NH2 is a capping 
residue, you need to interactively select termini (using the -ter option) and 
specify them as "None."  Otherwise, pdb2gmx treats all residues as normal amino 
acids and tries to build normal amino and carboxylate termini.

-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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