AMBER Archive (2008)

Subject: Re: AMBER: Querry

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Aug 27 2008 - 08:20:55 CDT

there should be no TER between the protein and peptide.

On Wed, Aug 27, 2008 at 5:00 AM, dipti lele <diptisl86_at_gmail.com> wrote:
> Hello,
>
> This is some more explanation for what I am doing. 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,
>
>
>
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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