On 2012-11-17 15:37, Atila Petrosian wrote:
Hi all.
After using amber03 force field for protein-ligand simulation (pdb2gmx), I
encountered with following error:
Fatal error:
In the chosen force field there is no residue type for 'GLN' as a starting
terminus.
Ligand in my system is a single residue (GLN). There are [GLN], [NGLN] and
[CGLN] in rtp file of amber03 force field. Should this single residue be as
both of [NGLN] and [CGLN]?
How to fix this error?
Any help will highly appreciated.
Manually making a toplogy is your best best. Add an alanine after the
gln then in the top file rename and remove atoms.
GAFF is an alternative but it will not give you exactly the same charges
and LJ parameters.
--
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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