Re: excluding water in dcd files

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Nov 03 2003 - 17:21:00 CST

Hi,

Your psfgen script looks fine (and quite typical). Perhaps you could
include a couple of lines from your output file showing your problem?

I can say that the PDB chain ID is column 22, between the three character
residue name and the four digit residue ID number. By reviewing the
psfgen source code I can tell you that this field is never used. The same
is true of the insertion code in column 28.

Psfgen uses the input PDB files only to extract sequence and coordinate
information. The beta, occupancy, etc. are not preserved for output.

-Jim

On Tue, 4 Nov 2003, himanshu chandola wrote:

> Hello everyone,
> i guess what jerry has suggested would do the work for me. Yet
> i have got what went wrong . The psfgen was giving me the file with chain
> ids changed to numbers. Now where could i have got wrong ?The following is
> my psfgen config file :
> resetpsf
> topology /home/himanshu/md/data/param/top_all27_prot_na.inp
> alias residue HIS HSD
> alias residue HOH TIP3
>
> alias atom ILE CD1 CD
> alias atom GLY OXT OT1
> segment A {
> pdb output/a.pdb
> }
> segment B {
> pdb output/b.pdb }
>
> segment C {
> pdb output/c.pdb }
>
> segment D {
> pdb output/d.pdb }
>
> segment E {
> pdb output/e.pdb }
>
> coordpdb output/a.pdb A
> coordpdb output/b.pdb B
> coordpdb output/c.pdb C
> coordpdb output/d.pdb D
> coordpdb output/e.pdb E
>
> guesscoord
>
> writepsf output/bov.psf
> writepdb output/bov.pdb
>
> thanks everyone again
>
> himanshu
>
>
> ----------------------------------------
> Morpheus: Do you believe in fate, Neo?
> Neo: No.
> Morpheus: Why Not?
> Neo: Because I don't like the idea that I'm not in control of my life.
>
>
> On Mon, 3 Nov 2003, Jerry Ebalunode wrote:
>
> > Hi,
> > What I normally do to this solve problem is to simply build an index file
> > decribing the indices for various atom entries in the pdb file using VMD in
> > your case protein atoms. This index file in combination with the CATDCD
> > program is then used to extract protein atom trajectories from the namd dcd
> > file. The output dcd file will contain trajectories of only the atoms that
> > you are interested in.
> >
> >
> > On Monday 03 November 2003 08:31 am, himanshu chandola wrote:
> > > dear namd users,
> > > is there any inbuilt functionality in namd wherein i have the
> > > option of whether the water molecules in my dcd files. This would make my
> > > work hell lot of easier because ultimately though i need to have the
> > > interaction of water molecules with my protein - i don't need to have
> > > their information stored in the dcd files .
> > >
> > > with kind regards,
> > >
> > > himanshu
> > > iit delhi
> > >
> > > ----------------------------------------
> > > Morpheus: Do you believe in fate, Neo?
> > > Neo: No.
> > > Morpheus: Why Not?
> > > Neo: Because I don't like the idea that I'm not in control of my life.
> >
> > --
> > Cheers,
> >
> > Jerry Ebalunode
> > Graduate Research Assistant
> > RM 402F Houston Science Center
> > Phone: 713-743-8367
> > Dept. of Biology and Biochemistry
> > University of Houston.
> > 4800 Calhoun Road
> > Houston, TX 77204
> >
> >
>

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