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

[David van der Spoel]

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