From: himanshu chandola (beu99419_at_ccsun50.iitd.ernet.in)
Date: Tue Nov 04 2003 - 02:00:18 CST
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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