Re: excluding water in dcd files

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Nov 04 2003 - 10:35:55 CST

see responses inside the text

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)
>
> 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 .

Was the wayward atom part of the protein or xtalization liquor? Or just
some extra ion that was not deleted? Use vmd to find out what this atom is!
Does the protein have a helix? VMD uses an auxillary program to calculate
secondary structure and by its definition there may not be a 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.
Don't bother with adding these ^^^^^^^^^ until you have solved a simpler
version of the problem. There is little info on AlF3 for classical MD,
allthough the other two molecules do exist in one form or another in the
charmm libraries. In 90% of MD papers published cofactors and inhibitors
are left out for simplicity. Start simple and work up when things make
sense.

> 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
> > > >
> > > >
> > >
> >
> >
>

-- 
*****************************************************************
**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448    bennion1_at_llnl.gov                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 422-6605                 **
*****************************************************************

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:17:53 CST