AMBER Archive (2006)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Jan 13 2006 - 04:40:56 CST

Dear Priti,

I think the reason is very obvious; your frcmod file is missing
the necessary parameters to describe the .pdb file. Your frcmod file is
created for the .prepin file. When your non-standard residue is in a
structure, it is bonded to at least one residue. And when it is bonded, u
need to describe the missing parameters. For instance, let's
say that the head atom of your non-standart residue is an 'S', with an
atom type 'sh'. This atom will have a bond with the next residue. And
let's say the tail atom of the next residue is a 'C' with an atom type
'C'. U need to describe, for instance, the bond length of 'sh-C'. This is
just the simplest case. U need to describe the missing angular and
dihedral parameters,etc. too.

Hope this helps. Good luck.

On Fri, 13 Jan 2006, Priti Hansia wrote:

>
> 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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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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