VMD-L Mailing List

From: Philip Blood (philb_at_hec.utah.edu)
Date: Fri Mar 11 2005 - 13:44:45 CST

Okay, it turns out that I just forgot about a formatting difference in
how pdb files are written in charmm and read into these utilities.
(Sorry, I hate it when I find the problem 5 minutes after posting.) :)
The residue number column is shifted over to the right when written from
charmm, so I was missing the first number on all residues after 999.

However, there is a problem with how residue numbers from the added
water boxes are written back out into the pdb and psf files. Certain
numbers are skipped so that a sequence might read 2,3,7,11 etc. I guess
the missing numbers are the waters that were cut out to avoid overlaps.
Has anyone looked at fixing this? As it is, maybe NAMD doesn't care
about sequential numbering, but I am not sure. It is probably a good
idea to renumber these sequentially.

 

Phil

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Friday, March 11, 2005 12:38 PM
To: Philip Blood
Cc: vmd-l_at_ks.uiuc.edu; vmd_at_ks.uiuc.edu; Jim Phillips
Subject: Re: vmd-l: limit on segment atom number in solvate and
autoionize

Phil,
  Can you tell me what error message(s) if any you are getting
when you try to do this? It should work fine as far as I know.
If you encounter a problem with the number of atoms in a segment,
number of segments, etc, they are likely to be issues with the
'psfgen' plugin, not with the solvate/autoionize plugins themselves,
since they use psfgen for most of the heavy lifting they do.
If you can send me more information on what's happening, it'll
help narrow down if this is in fact 'psfgen' or some buglet in
the other plugins you mentioned.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 11, 2005 at 12:18:22PM -0700, Philip Blood wrote:
> Correction: I thought I had seen this behavior in autoionize, but it
> looks like it only occurs in the solvate plugin. I am using VMD 1.83
> and running solvate from the command line.
>
> Phil
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
Behalf
> Of Philip Blood
> Sent: Friday, March 11, 2005 10:53 AM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: limit on segment atom number in solvate and autoionize
>
> Hi,
>
> The solvate and autoionize plugins can only read in coordinates for
999
> atoms in a given segment even though the charm default is (a much more
> convenient) 9999. Is there any way around this limitation besides
> chopping up the system into segments of 999? Is there a reason why it
> is done this way and could it be easily changed?
>
> Thanks,
> Phil Blood 

-- 
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