From: himanshu chandola (beu99419_at_ccsun50.iitd.ernet.in)
Date: Tue Nov 04 2003 - 11:45:28 CST
Hello,
the following are some lines of how my pdb file looked like and how it
did after having psfgen used. In the psfgen i made one segment each for
each chain.
pdb file before:
ATOM 1 N ALA A 19 51.074 165.718 79.087 1.00 97.57
ATOM 2 CA ALA A 19 52.097 165.982 78.087 1.00 97.37
ATOM 3 C ALA A 19 53.269 165.014 78.232 1.00 96.96
ATOM 4 O ALA A 19 53.164 163.786 78.194 1.00 98.84
after:
ATOM 1 N ALA 19 51.074 165.718 79.087 1.00 0.00 A
ATOM 2 HT1 ALA 19 50.142 165.995 78.853 0.00 0.00 A
ATOM 3 HT2 ALA 19 51.533 166.452 79.588 0.00 0.00 A
ATOM 4 HT3 ALA 19 51.053 164.887 79.644 0.00 0.00 A
(in the above generated pdb file - the A on the extreme right might be the
segment name - i have put these molecules in segment A)
I have another point to ask. I need to remove some inhibitors and other
molecules used in crystallization. I removed these molecules in the
original pdb file itself(by manual deletion) but after having generated a
psf file from such a molecule, I found one of my atoms to be wayward from
the rest of the protein. Also the cartoon of the protein generated by the
vmd looked awkward with no helix .
Hence I planned to generate a pdb and psf file for the original protein
itself(and use delatom in the vmd later) but there the problem is that I
don't have parameters for GOL,AlF3,SO4.
Can anyone suggest a remedy please?
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, Jim Phillips wrote:
> 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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