On 2012-11-18 10:40, Atila Petrosian wrote:
Dear David
Thanks for your attention.
I have 2 problems/questions:
1) There are a specific orientation for GLN ligand with regard to protein
in my system. If I do what you said [you make a separate molecule Gln-Ala
using pymol or vmd], specific orien
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
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 res
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