VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Tue Dec 26 2006 - 14:49:45 CST

Dear all,
I want to split a pdb into several segments for later use with psfgen.
The problem that I am facing is that for each segment that I write into
a new pdb, I get an additional X in the chain column. In the original
pdb there were no chain identifiers. This results on a problem when
reading the coordinates from the new pdb with coordpdb in psfgen.

This is the script that I use to split the pdb

set all [atomselect top all]
set lseglist [lsort -unique [$all get segid]]
foreach lseg $lseglist {
    set selover [atomselect top "segid $lseg"]
    $selover writepdb $lseg.pdb
}

A line from the original PDB file

ATOM 26852 CLA CLA 2 31.223 -0.301 20.128 1.00 0.00 BCL

The same line in the final PDB. Note that the chain identifier was added
by vmd.

ATOM 1 CLA CLA X 2 31.223 -0.301 20.128 1.00 0.00
BCL

How may I instruct VMD to write pdb without chain identifier?
Regards
Cesar