AMBER Archive (2008)

Subject: Re: AMBER: Querry

From: dipti lele (diptisl86_at_gmail.com)
Date: Wed Aug 27 2008 - 08:33:45 CDT

Oh sorry i was supposed to write no TER..

On Wed, Aug 27, 2008 at 10:20 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> 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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> 

-- 
Deepti Lele,
NII, New Delhi.

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