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.
Mark
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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