No, I nave not obtained any results even after all night calculations. MAy
be you are right and something is wrong (((( I'll use your advices...Thank
you D.A.C.
2011/10/17 David A. Case <case.biomaps.rutgers.edu>
> On Mon, Oct 17, 2011, Алексей Раевский wrote:
>
> > Hi, when i used antechamber to create a topology file for cyclospoorine
> > (cyclopeptide with metilated residues...) it had run the command and I
> 've
> > got such "warnings" for several non-standart residues of this peptide:
> > --------------------------------------
> > antechamber -i d_h.mol2 -fi mol2 -o d_a.mol2 -fo mol2 -c bcc -s 2
> > Running: /opt/software/amber/amber11//bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> >
> > -- Judge bond type for Residue 1 with ID of 1 and Name of ...
> > -- Judge bond type for Residue 2 with ID of 2 and Name of ...
>
> This is not necessarily an error, but you should certainly check the output
> atom types to see if they make sense.
>
> Did the sqm job finish, and did you get the d_a.mol2 file?
>
> It is more typical to build non-standard peptides by modifying the standard
> ones (and hence using Amber atom types, not gaff ones). If you google on
> something like "cyclosporin molecular dynamics" you can see what others
> have
> done; (maybe you have already done this, though).
>
> ...dac
>
>
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Received on Sun Oct 16 2011 - 23:00:03 PDT
