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

2012-11-18 Thread David van der Spoel
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

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

2012-11-17 Thread 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

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

2012-11-17 Thread David van der Spoel
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