[gmx-users] acylation of peptide

Mark Abraham Mark.Abraham at anu.edu.au
Tue Oct 18 00:50:47 CEST 2011

On 18/10/2011 2:57 AM, ??????? ???????? wrote:
> 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?

If the atom types and interactions for the acylated peptide can be found 
in a regular force field, then the simplest approach is to create a new 
residue for the force field of interest using a text editor, following 
the instructions on the GROMACS website. Knowledge of chapter 5 of the 
manual will be essential.


> On 17/10/2011 5:01 PM, ??????? ???????? wrote:
> > Hi!
> > 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.
> Mark

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