AMBER Archive (2006)

Subject: AMBER: problem imposing arbitrary peptide bonds through leap

From: Amarda Shehu (shehua_at_cs.rice.edu)
Date: Mon Aug 14 2006 - 11:27:24 CDT

Hello,

I have just installed amber9 and am quite new to the amber force field (I have
up to now used CHARMM).

I want to construct a short peptide chain, adding peptide bonds as seeing fit.
When I try to form a peptide bond between residue x and residue y with the
command BOND mol.x.C mol.y.N, I get the following:
  Building proper torsion parameters.
  ** No torsion terms for CT-N3-C-CT
  ** No torsion terms for CT-N3-C-O2
  ** No torsion terms for CT-N3-C-O2
  ** No torsion terms for H-N3-C-CT
  ** No torsion terms for H-N3-C-O2
  ** No torsion terms for H-N3-C-O2
  ** No torsion terms for H-N3-C-CT
  ** No torsion terms for H-N3-C-O2
  ** No torsion terms for H-N3-C-O2
  ** No torsion terms for H-N3-C-CT
  ** No torsion terms for H-N3-C-O2
  ** No torsion terms for H-N3-C-O2

I am not sure how to suppress amber from adding hydrogens first of all to my
initial pdb file, and then how to tell it to add a peptide bond between two
arbitrary residues.

Any help will be greatly appreciated, as I have not been able to find any
information on google or the faq page in amber.scripps.edu.

Thank you.
***********************************
Amarda Shehu,
Graduate Student, Computer Science,
Rice University.
***********************************
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