VMD-L Mailing List

From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Thu Jan 15 2009 - 09:25:23 CST

Javier,

I normally do not use psfgen directly... instead I do it the following
way

topology some_file.top

set ID Quartz
mol new ${ID}.pdb

set seg1 SLAB
set prot [atomselect top all]
$prot set segname $seg1

$prot writepdb pdbfile.pdb

mol delete all

segment ${seg1} {
first none
last none
pdb pdbfile.pdb }

coordpdb pdbfile.pdb

writepsf New_file.psf
writepdb New_file.pdb

exit

Doing this removes the "guesscoord" command that would generate the
missing atoms, you do not want.

There may be more elegant solutions while still using psfgen :).

Hope this helps

Chris

On Jan 15, 2009, at 9:03 AM, Javier Goicochea wrote:

> Hi all,
>
> I am trying to use correctly topology files. The molecular system I
> am building is composed by different substances: solids and liquids,
> for example (but not limited to) Quartz and Water or Silicone. So
> far, I can create PDB files for the different geometries and
> substances to be studied. However, I do not have the topology files
> for Quartz, nor for the other solids I want also to study. I am
> basically interested in using psfgen in VMD to create the PSF file,
> but I need the topology file.
>
> At this point, I have been trying to understand the structure /
> format of the topology file and I have managed to create a simple
> (initial) version of the topology file for Quartz. This topology
> file can create the PSF file, with bonds, angles and dihedrals.
>
> The main problem I am facing is the following. Quartz structure (low
> quartz) is given by a lattice representation (i.e. all atomic
> positions are given by the lattice vectors and the difference basis
> (9)) and belongs to the trigonal crystal system. However, my
> geometry is in Cartesian coordinates, hence, the crystal structure
> is trimmed to conform to the boundaries of my geometry (3D). During
> the trimming of the boundaries, some units cells also trimmed,
> therefore they have less than 9 atoms. When I try to use the
> topology file, psfgen typically creates more atoms (multiple of 9)
> that those originally in the PDB file. I suspect patches are
> required to handle different boundary situations.
>
> For example, if I have 100 atoms in my PDB and 16 residues (unit
> cells for me), the psfgen creates 144 atoms in the PSF file.
> Obviously psfgen follows the topology file structure, since, Quartz
> is represented there with 9 different atoms (3 Si and 6 O).
>
> Here are the TOP and PDB files:
>
> > * My Topology file JGP
> > *
> > 18 1
> > MASS 1 HT 1.00800 H ! H Atom
> > MASS 2 OT 15.99940 O ! O Atom
> > MASS 3 SI 28.08550 SI ! Si Atom
>
> > AUTO ANGLES DIHE
> > RESI Q100 0.000
> > GROUP
> > ATOM O1 OT -0.530
> > ATOM O2 OT -0.530
> > ATOM O3 OT -0.530
> > ATOM O4 OT -0.530
> > ATOM O5 OT -0.530
> > ATOM O6 OT -0.530
> > ATOM SI1 SI 1.060
> > ATOM SI2 SI 1.060
> > ATOM SI3 SI 1.060
> > BOND O5 SI1 O2 SI2 O3 SI1 O6 SI3
> > BOND O1 SI1 O3 SI2 O4 SI3 O5 SI3
> > PATCHING FIRST NONE LAST NONE
> > END
>
> Please ignore the BOND connectivity, at the moment.
>
> > ATOM 1 SI1 Q100 1 A 0.231 0.000 0.450 1.00 0.00
> > ATOM 2 SI2 Q100 1 A -0.115 0.200 0.270 1.00 0.00
> > ATOM 3 SI3 Q100 1 A 0.130 0.226 0.090 1.00 0.00
> > ATOM 4 O1 Q100 1 A 0.138 0.114 -0.064 1.00 0.00
> > ATOM 5 O2 Q100 1 A 0.324 0.062 0.296 1.00 0.00
> > ATOM 6 O3 Q100 1 A 0.030 0.176 0.244 1.00 0.00
> > ATOM 7 O4 Q100 1 A 0.276 0.249 0.116 1.00 0.00
> > ATOM 8 O5 Q100 1 A -0.108 0.311 0.425 1.00 0.00
> > ATOM 9 O6 Q100 1 A 0.078 0.363 0.064 1.00 0.00
> > ATOM 10 SI1 Q100 2 A 0.231 0.000 0.991 1.00 0.00
> > ATOM 11 SI2 Q100 2 A -0.115 0.200 0.811 1.00 0.00
> > ATOM 12 SI3 Q100 2 A 0.130 0.226 0.631 1.00 0.00
> > ATOM 13 O1 Q100 2 A 0.138 0.114 0.476 1.00 0.00
> > ATOM 14 O2 Q100 2 A 0.324 0.062 0.837 1.00 0.00
> > ATOM 15 O3 Q100 2 A 0.030 0.176 0.785 1.00 0.00
> > ATOM 16 O4 Q100 2 A 0.276 0.249 0.657 1.00 0.00
> > ATOM 17 O5 Q100 2 A -0.108 0.311 0.965 1.00 0.00
> > ATOM 18 O6 Q100 2 A 0.078 0.363 0.605 1.00 0.00
> > ATOM 19 SI1 Q100 3 A 0.231 0.000 1.531 1.00 0.00
> > ATOM 20 SI2 Q100 3 A -0.115 0.200 1.351 1.00 0.00
> > ATOM 21 SI3 Q100 3 A 0.130 0.226 1.171 1.00 0.00
> > ATOM 22 O1 Q100 3 A 0.138 0.114 1.017 1.00 0.00
> > ATOM 23 O2 Q100 3 A 0.324 0.062 1.377 1.00 0.00
> > ATOM 24 O3 Q100 3 A 0.030 0.176 1.325 1.00 0.00
> > ATOM 25 O4 Q100 3 A 0.276 0.249 1.197 1.00 0.00
> > ATOM 26 O5 Q100 3 A -0.108 0.311 1.506 1.00 0.00
> > ATOM 27 O6 Q100 3 A 0.078 0.363 1.145 1.00 0.00
> > ....
>
> Here the PDB file shows 9 atoms per residue (per unit cell), but in
> general, there can be less than 9.
>
> How I should deal or remove correctly these extra atoms created in
> the PSF file by psfgen? Should I have to include patches for the
> different surfaces?
>
> Feel free to comment or provide suggestions?
>
> Regards, Javier
>