VMD-L Mailing List

From: Thomas Caulfield (thomas.caulfield_at_chemistry.gatech.edu)
Date: Sat Aug 19 2006 - 22:35:55 CDT

Hi John Stone and VMD-Lers,

I am wondering what the work-around is for the psfgen when I want to
solvate with more than WT99 for the segname. I am making a very
large solvated system, and when I did a smaller one of up to WT51, I
was okay. Perhaps there is a way to change the psfgen name for
waters to W instead of WT for the segname? Then I could at least go
up to W999. It seems like the WT# size for number of atoms per
segname is rather variable too. In my earlier WTs, WT8 or WT17 the
number of atoms is in the 4500 range, yet with WT50 I am getting over
25,000 atoms. If I could just enforce every segname to be that
large, there would be no problem.

Thanks for any insight into how to do this is much appreciated.

Sincerely,
-Tom

PS I did examine the VMD-L list, and below is the most closely
related topic.

****************************************
Tom Caulfield, Ph.D. Candidate
School of Chemistry & Biochemistry
Cherry Emerson Bldg., RM 329
Georgia Institute
ofTech nology
Atlanta, GA 30332-0400
Harvey Laboratory:
http://rumour.biology.gatech.edu
****************************************

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 11 2005 - 13:38:23 CST
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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