AMBER Archive (2008)

Subject: AMBER: querry

From: dipti lele (diptisl86_at_gmail.com)
Date: Wed Aug 27 2008 - 04:07:52 CDT

Hello,

   This is some more explanation for what I am doing with the reference to
my previous querry about adding a peptide to the C terminal region of the
protein. I have a protein and its C terminal end is short. I need to add few
residues at the C terminal end. thus I have a protein and a small peptide
which I have to join. I have oriented them nearby. There is TER and also
changed the numbers of atoms accordingly. ( REsidues from 608 are peptide).

Now when I load such pdb file it is making the terminal residues and added
extra H and OH. Now when I say bond command and try to top and crd file I
get

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - N3
Building angle parameters.
Could not find angle parameter: O2 - C - N3
Could not find angle parameter: O2 - C - N3
Could not find angle parameter: C - N3 - H
Could not find angle parameter: C - N3 - H
Could not find angle parameter: C - N3 - H
Could not find angle parameter: C - N3 - CT
Could not find angle parameter: CT - C - N3
Building proper torsion parameters.
 ** No torsion terms for O2-C-N3-H
 ** No torsion terms for O2-C-N3-H
 ** No torsion terms for O2-C-N3-H
 ** No torsion terms for O2-C-N3-CT
 ** No torsion terms for O2-C-N3-H
 ** No torsion terms for O2-C-N3-H
 ** No torsion terms for O2-C-N3-H
 ** No torsion terms for O2-C-N3-CT
 ** No torsion terms for CT-C-N3-H
 ** No torsion terms for CT-C-N3-H
 ** No torsion terms for CT-C-N3-H
 ** No torsion terms for CT-C-N3-CT
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for CT-O2-C-N3
        atoms are: CA O C N
 ** Warning: No sp2 improper torsion term for CT-O2-C-N3
        atoms are: CA OXT C N
 total 685 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.

what must have gone wrong?

How should I proceed?

Thanking you,
With regards, 

-- 
Deepti Lele,
NII, New Delhi.

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