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On 18/10/2011 2:57 AM, Алексей Раевский wrote:
<blockquote
cite="mid:CAB6CZ-=3Q53gjKoJGpRYAec7U8-fXp17+=YAi3an4Miq-5PGOg@mail.gmail.com"
type="cite">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?<br>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAB6CZ-=3Q53gjKoJGpRYAec7U8-fXp17+=YAi3an4Miq-5PGOg@mail.gmail.com"
type="cite">
<br>
<br>
On 17/10/2011 5:01 PM, Алексей Раевский wrote:<br>
> Hi!<br>
> I need an advice concerninng topology building of such
substance like<br>
> cyclosporine A. I've tried to make it with antechamber tool,
cause I<br>
> wanted to use amber99sb forcefield. But the program gave me
an error<br>
> in the begining and no results in the end after 12 hours of<br>
> calculations ))) Can you give any suggestions for my next
steps? This<br>
> compound is a peptide chain built from acyl-adenylated amino
acids<br>
> (L-valine, L-leucine, L-alanine, L-glycine, 2-aminobutyric
acid,<br>
> 4-methylthreonine, and D-alanine).<br>
> Thank you very much!<br>
<br>
If you're asking for antechamber help, you're on the wrong forum.<br>
<br>
Mark<br>
<br>
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