[AMBER] ligand-protein complex parametrization problems

From: Andrew Voronkov <drugdesign.yandex.ru>
Date: Thu, 11 Mar 2010 18:39:52 +0300

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,

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.

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Received on Thu Mar 11 2010 - 08:00:03 PST
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