VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 07 2008 - 11:54:54 CDT

Hi,
  Can you send me the exact structure files and commands needed to
replicate your problem? We had asked Cesar to provide this information
previously, but never got any reply, so we were never able to reproduce
the problem. (and thus it didn't get fixed)
The only bugs that get fixed are the ones that we're able to reproduce.

>From the sound of it, this is actually an issue with psfgen and not VMD,
but we'll still need the structure files and command sequence you used
that let to the trouble.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 07, 2008 at 06:31:52PM +0800, Low Soo Mei wrote:
> 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078