VMD-L Mailing List

From: Low Soo Mei (lowsm_at_bii.a-star.edu.sg)
Date: Mon Apr 07 2008 - 05:31:52 CDT

Hi VMD users,

I have had the same problem as Cesar described here
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8395.html in Dec
2006, but my VMD version is 1.8.6 for Linux OpenGL, so it appears that
the bug reported there by Cesar has not been fixed yet...

In any case I have resolved the problem of the extra X altering the
resid positions the same way as Cesar did, by hand-deleting the resname
X column. Much thanks to him and to the list for being available online
to Google!

Briefly, my system had 6831 waters and I could not get the psf generated
with the correct number of waters by either AutoPSF or by psfgen. I
then thought the waters might be too numerous to be taken as one segment
and remembered seeing something about using only 999 waters per segment,
so I hand-separated them into segments of 999 waters each, giving each
segment a different segname. Then I used VMD atomselect to write out
each of these segments to their own pdb file each. And thereafter I
tried psfgen again. The results are: Psfgen was only able to read in
the first segment of 999 waters and then thereafter truncated all my
remaining six 999-water segments to read only 100 or 101 waters each
when building the segments. Segment-building, coordpdb, and
writepsf/writepdb went smoothly for all segments with no errors, aside
from the 100 or 101 waters seen in the tkconsole. When I opened the
original 999-water segment pdb files I had written out by VMD
atomselect, all had 999 waters and an X column tacked on to the resname
by VMD. When I opened the final erroneous pdb file, as described the
first 999-water segment had all waters present but the following six
segments had only 100 or 101 waters present, and all seven segments
still had the X column as well. I noticed the 2nd digit of all the
4-digit resids had been truncated such that e.g. my 2014th residue of
water was only "214". And I had lots of waters missing because of this
resid issue.

I then went back to my segment pdb files that VMD atomselect had written
out, and hand-deleted the X column tacked on to the resname by VMD. I
tried psfgen again and this time all my waters were present in the final
psf and pdb. I left the X column untouched throughout in the other
components of my system (the lipids, the ions) and no complications
ensued from that.

Perhaps this email is too long, but it was initially very frustrating
wondering why my waters had disappeared somewhere between segment
building and the final psf/pdb, in the innards of psfgen. I had spent a
long time reading through various VMD and NAMD mails on the mailing list
before finding Cesar's that helped me. The mails regarding the solvate
and autoionize plugins were not applicable to my system because it was
already nicely solvated and ionized, previously created by someone else
:) I simply needed the psf from it. I hope this email has succeeded in
having all the relevant keywords implanted in it :) such that I wish it
may help others with the same problem.

Thank you for your time and kind attention.

Cheers,
Soo Mei