change segID using segment command in psfgen

From: Low Soo Mei (lowsm_at_bii.a-star.edu.sg)
Date: Thu Mar 06 2008 - 03:01:18 CST

Dear NAMD users,

This is not a scientific query, but a scripting query. I would like to
ask: The NAMD 2.6 (latest) user guide pg 39 says that the coordpdb
command in the psfgen package can "override segment IDs in PDB file".
However, when I used that to try to override my input PDB file's segID,
it did not work, as below.

topology toppar/top_all22_prot.inp
segment DMPG {
pdb membrane.pdb
}
coordpdb membrane.pdb DPPC
(massive error output for every atom, saying "no segment DPPC found")

When I instead specified the new segID I wanted using the segment
command, during the 'Build protein segment' part and inspected the
output mem_test psf and pdb files in vi, it seems to have worked, as below.

topology toppar/top_all22_prot.inp
segment DPPC {
pdb membrane.pdb
}
coordpdb membrane.pdb DPPC
(no error output)
guesscoord
writepsf mem_test.psf
writepdb mem_test.pdb

Have I perhaps been using coordpdb wrongly? Or should the changing of
segID indeed be done using the segment command?

I have been trying to find a general way to change the segID within VMD
instead of doing it by hand, for some time.

Many thanks for your advice.

Cheers,
Soo Mei

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