Re: Counting H-bonds from a dcd file

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue Aug 29 2006 - 18:48:29 CDT

Have a look at the "measure hbonds" feature of VMD:

http://www.ks.uiuc.edu/Research/vmd/current/ug/node124.html

Gianluca

On Tue, 29 Aug 2006, Nitin Bhardwaj wrote:

> Dear NAMD users,
>
> I was wondering if there is a quick way to count the number of
> hydrogen bonds between a lipid molecule and a protein chain directly
> from the dcd file. I also want to use different paprameters for
> H-bonds (60 degrees as angle and 3.5 Ang as the distance cut-off).
>
> thanks a lot in advance.
> Rgds,
> Nitin
>
> On 03/08/06, Jerome Henin <jhenin_at_vitae.cmm.upenn.edu> wrote:
> > Sukesh,
> >
> > You can very easily generate a waterbox and the associated topology (PSF
> > format) with the Solvate plugin of VMD. In VMD use the menu item
> > Extensions->Modeling->Add solvation box, and specify no input files, but
> > check
> > the "waterbox only" box.
> > See a description there:
> > http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/
> >
> > Jerome
> >
> >
> > On Thursday 03 August 2006 14:19, Shenoy, Sukesh wrote:
> > > I want to generate the psf file for simulating a 1000 water molecules. The
> > > problem is that NAMD requires that the psf contain the bonds, angles and
> > > dihedral information for all the 1000 water molecules. It is cumbersome
> > > and
> > > time consuming to do this manually. Does anybody know how one can do this
> > > quickly (through a program perhaps)?
> > >
> > > Sukesh
> >
>
>
> --
> [a6][ad]I+I[a7][aa]
>

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                    +1 (206) 714 4303
                    http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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