AMBER Archive (2009)

Subject: [AMBER] problem with parametrization

Date: Wed Jun 24 2009 - 13:24:45 CDT

Dear Everyone!

I am trying to create a non-standard residue with antechamber to use
it in tleap. This residue is the isopeptide form of the gly-ser
dipeptide, where the carbonyl group of the glycine is attached to the
-OH group of the serine sidechain. I have created and parametrized
this molecule following the antechamber tutorial for creating
non-standard residues, I also created an frcmod file with parmchk. But
when I try to build a polipeptide chain using my new residue, leap
complains about missing parameters. Basically the missed parameters
are at the joining points of my residue with the rest of the
The message goes like this (I built a tripeptide in this example after
loading leaprc.gaff and leaprc.ff99SB):

> loadamberparams glyser.frcmod
Loading parameters: ./glyser.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> loadamberprep glyser.prepi
Loading Prep file: ./glyser.prepi
> aa = sequence { ALA GSD ALA }
> saveamberparm aa proba.prmtop proba.inpcrd
Checking Unit.
ERROR: The unperturbed charge of the unit: -0.107460 is not integral.
WARNING: The unperturbed charge of the unit: -0.107460 is not zero.

  -- ignoring the error and warning.

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - n
Could not find bond parameter for: c - N
Building angle parameters.
Could not find angle parameter: O - C - n
Could not find angle parameter: C - n - hn
Could not find angle parameter: C - n - c3
Could not find angle parameter: CT - C - n
Could not find angle parameter: o - c - N
Could not find angle parameter: c - N - H
Could not find angle parameter: c - N - CT
Could not find angle parameter: c3 - c - N
Building proper torsion parameters.
  ** No torsion terms for O-C-n-hn
  ** No torsion terms for O-C-n-c3
  ** No torsion terms for CT-C-n-hn
  ** No torsion terms for CT-C-n-c3
  ** No torsion terms for o-c-N-H
  ** No torsion terms for o-c-N-CT
  ** No torsion terms for c3-c-N-H
  ** No torsion terms for c3-c-N-CT
Building improper torsion parameters.
old PREP-specified impropers:
  <GSD 2>: C3 O2 C4 O3
  <GSD 2>: +M C6 C7 O4
  total 5 improper torsions applied
  2 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved."

Since I want to use the force field ff99SB for my calculations, and
the isopeptide residue was parametrized using gaff the missing
parameters are aviable at both force field, but not recognized because
of the capitalization. I figured I can modify the frcmod file to have
leap handle these angles and bonds and dihedrals, but I could not find
some of the dihedral parameters, neither in parm99.dat or gaff.dat:

Could you tell me where can I find these parameters, or what
parameters should I use?

Thanks in forward:
Gabor Janzso

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