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.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Aug 31 2008 - 06:07:05 PDT
