[gmx-users] Re: gmx-users Digest, Vol 90, Issue 82
rayevsky85 at gmail.com
Mon Oct 17 17:57:42 CEST 2011
No I need your help in any way, antechamber is not only the way I could do
it, I think...I just showed you that I tried something before I wrote you a
letter. It is not necessary to use amber forcefield, but I don't think that
prodrg is a good choice for this task, though the only modification of the
residues in the peptide is acylation. But may be you know something! Thank
you very much?
On 17/10/2011 5:01 PM, Алексей Раевский wrote:
> I need an advice concerninng topology building of such substance like
> cyclosporine A. I've tried to make it with antechamber tool, cause I
> wanted to use amber99sb forcefield. But the program gave me an error
> in the begining and no results in the end after 12 hours of
> calculations ))) Can you give any suggestions for my next steps? This
> compound is a peptide chain built from acyl-adenylated amino acids
> (L-valine, L-leucine, L-alanine, L-glycine, 2-aminobutyric acid,
> 4-methylthreonine, and D-alanine).
> Thank you very much!
If you're asking for antechamber help, you're on the wrong forum.
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