[gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

David van der Spoel spoel at xray.bmc.uu.se
Sat Nov 17 17:17:07 CET 2012

On 2012-11-17 16:26, Atila Petrosian wrote:
> Dear David
> Thanks for your quick reply.
> You said "Add an alanine after the gln then in the top file rename and
> remove atoms".
> I confused. Why ALA? ALA (alanine) is a residue which is very simple than
> GLN structurally.
> I should add alanine after the gln. But in which file?
you make a separate molecule Gln-Ala using pymol or vmd and then run it 
through pdb2gmx, this will give you NGLN-CALA. Then you edit the top 
file (remove superfluous alanine atoms, rename the N in ALA to O2 etc) 
with a text editor until it is "correct" with help from the rtp file for 
CGLN. You may have to smooth the charges to keep it neutral.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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