From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Nov 05 2003 - 13:36:37 CST
Hi,
On Tue, 4 Nov 2003, himanshu chandola wrote:
> 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)
This is correct. The far right is the segment name, "A". As I explained
below, the chain id "A" in your input is ignored by psfgen and replaced
with " " on output. If not having the chain id preserved bothers you, the
following VMD incantation should help:
[atomselect top "segid A"] set chain A
[atomselect top "segid B"] set chain B
[atomselect top "all"] writepdb withchains.pdb
If your wayward atom is at 0. 0. 0. then psfgen was unable to load or
guess coordinates for it. There should have been warnings printed about
this, and the occupancy field will be set to -1.0 (vs 1.0 for coordinates
read from a file and 0.0 for guessed coordinates).
-Jim
>
> 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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