AMBER Archive (2006)

Subject: AMBER: problem in saving parameter file for non-standard residue

From: Priti Hansia (priti_at_mbu.iisc.ernet.in)
Date: Fri Jan 13 2006 - 03:58:04 CST

Dear Amber users,

I have built the prepin and frcmod files for a non-standard residue using
antechamber. I am able to create the prmtop file for this residue. But
when I try to create the prmtop while for the PDB containing this residue
I get following problem:

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - sh
Could not find bond parameter for: o - N
Building angle parameters.
Could not find angle parameter: O - C - sh
Could not find angle parameter: C - sh - hs
Could not find angle parameter: C - sh - c3
Could not find angle parameter: CT - C - sh
Could not find angle parameter: o - N - H
Could not find angle parameter: o - N - CT
Could not find angle parameter: c1 - o - N
Building proper torsion parameters.
 ** No torsion terms for O-C-sh-hs
 ** No torsion terms for O-C-sh-c3
 ** No torsion terms for CT-C-sh-hs
 ** No torsion terms for CT-C-sh-c3
 ** No torsion terms for c1-o-N-H
 ** No torsion terms for c1-o-N-CT
 ** No torsion terms for c3-c1-o-N

and the parameter file is not saved !

I have only one S atom in PDB which actually belongs to the non-standard
residue. I don't understand why parameter file is not created when I use
the non-standard residue in the pdb. My PDB has 79 residues and
non-standard residue is at 37th position. I am using amber7.

Any kind of suggestion will be of great help to me.

Thanks,

-Priti

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