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 - 18:30:03 PDT
