[gmx-users] Regarding defining termini in new rtp entry

[Justin A. Lemkul]

Joe Joe wrote:
> How do I tell pdb2gmx what the termini are in my molecule. I added a non 
> standard amino acid to the ffoplsaa.rtp database but pdb2gmx says "No N- 
> or C-terminus found: this chain appears to contain no protein".

Add the new residues to aminoacids.dat, so that they are detected as protein.

-Justin

> 
> thanks,
> 
> Ilya
>  
> 

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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