VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 11 2005 - 15:13:12 CST

I asked Jim, and he says indeed NAMD doesn't care about sequential
numbering...

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 11, 2005 at 12:44:45PM -0700, Philip Blood wrote:
> 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 

-- 
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