On Thu, Feb 16, 2012, Yasuo Kurita wrote:
> I am trying to make an equilibrium calculation of 1EMB.pdb for preparing
> Gaussian09 code
> "SAC-CI ONIOM" calculation of GFP chromophore to get a light emitting spectra.
> The Residue type of chromophore is CRO which is not a standard Amino
> acid residue.
> So "saveamberparm" command reject to make the top and res files.
We need lots more information: exactly what you did, and what the exact
error message is. All you say above is that saveAmberParm fails: no one could
help with so little information.
As a guess: if you just read in a PDB file with an unknown residue (CRO),
saveAmberParm will fail. See the antechamber chapter in the Users' Manual, or
tutorial B4 for instructions on how to set up a ligand. This is mainly for
non-covalent linkages, but it might be a good start.
....good luck...dac
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Received on Thu Feb 16 2012 - 06:00:02 PST
