The ligand contains parameters that are not defined in the AMBER force field
you are utilizing. You should use antechamber and parmchk to define these
parameters in prepin and frcmod files. There is a good tutorial explaining
the steps involved here (
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_five/create_prmtop.htm
).
Good luck!
-Bill Miller
On Thu, Mar 11, 2010 at 10:39 AM, Andrew Voronkov <drugdesign.yandex.ru>wrote:
> Dear Amber users,
> I have problem while saving parametrization for protein-ligand complex. I
> remember that I ve solved once somehow this problem and it is related either
> to ligand formatting or hydrogens etc. But I can't remember how I ve solved
> it. Here is the ligand file and error log. I can also send PDB of protein
> but it seems to be ok with other ligands.
>
> Best regards,
> Andrew
>
>
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: cf - br
> Building angle parameters.
> Could not find angle parameter: br - cf - cf
> Could not find angle parameter: ce - cf - br
> Could not find angle parameter: ce - c3 - c2
> Could not find angle parameter: ce - c3 - h1
> Could not find angle parameter: ce - c3 - n3
> Building proper torsion parameters.
> ** No torsion terms for ce-ce-c3-c2
> ** No torsion terms for ce-ce-c3-h1
> ** No torsion terms for ce-ce-c3-n3
> ** No torsion terms for c2-ce-c3-c2
> ** No torsion terms for c2-ce-c3-h1
> ** No torsion terms for c2-ce-c3-n3
> Building improper torsion parameters.
> total 814 improper torsions applied
> Building H-Bond parameters.
> Parameter file was not saved.
> Quit
>
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>
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Received on Thu Mar 11 2010 - 08:00:03 PST
