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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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