Can we do this with a pdb file? i.e. generate a list of pair of residue
names/IDs between which there are backbone H-bond?
Thanks for your suggestions.
On Mon, Sep 17, 2012 at 6:08 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Why not just use the hbond command? In cpptraj something like 'hbond
> .C,N,H,O avgout hbavg.dat' should work.
>
> -Dan
>
> On Monday, September 17, 2012, vaibhav dixit wrote:
>
> > Dear Amber users,
> > I'm using secstruct command for making secondary structure prediction.
> > Manual says that it uses DSSP program. My question is...
> > Can DSSP program be used to print a list of pair of AA residue names/IDs
> > that form backbone H-bonds in a given protein sequence?
> > It does seem to calculate/use this information for giving the usual
> output
> > files.
> >
> > Thanks for your help and suggestions in advance.
> >
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D. Scholar
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408
> > E-mail: vaibhavadixit.gmail.com <javascript:;>
> > www.niper.nic.in
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Mon Sep 17 2012 - 21:00:03 PDT
