From: Θωμας Ευαγγελιδης (te8624_at_mbg.duth.gr)
Date: Mon Aug 13 2007 - 16:26:27 CDT

Hi,

is it feasible to create psf and dcd files from a set of pdb files, all
containing the same atoms? I created these pdbs from an initial pair of psf and
dcd files by deleting some atoms and moving some others with the "moveby"
command. Each pdb represents a modified frame of the initial trajectory.
I have tried the "autopsf" command but it creates a psf with a slightly higher
number of atoms (about 5750 while each pdb contains only 5315), so I can't
use the dcd created with the simple text command:
set sel [atomselect top all]
$sel writedcd frame1.dcd

It is also remarkable that when I created a dcd from the pdb file made
by autopsf command (wich also contains 5750 atoms) and then used it together
with the psf, the emerging molecular system was an identical copy of that
contained in the original pdb except from some additional lines which were all
starting from the same point but were expanding on different directions. Can
anybody suggest a solution?
I would appreciate any help,
Thomas Evangelidis

P.S.:please don't tell me just to load the pdb files into VMD and simulate an
animation. I strictly need to create a new pair of psf and dcd files from this
set of pdbs!