VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sat Aug 19 2006 - 23:30:06 CDT

Hi Tom,

I'm also solvating a very big system, and I simply switched from 'WT'
to 'W'. At least for me it works perfectly. I need to build at least
300 water layers around my protein and get a fairly big system. I
don't know if anybody has gone beyond the 999 layers, so I think this
"change" should work for you :)

Cheers,
Michel

2006/8/19, Thomas Caulfield <thomas.caulfield_at_chemistry.gatech.edu>:
>
> 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
> Next message: Philip Blood: "RE: limit on segment atom number in solvate and
> autoionize"
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> and autoionize"
> In reply to: Philip Blood: "RE: limit on segment atom number in solvate and
> autoionize"
> Next in thread: Philip Blood: "RE: limit on segment atom number in solvate
> and autoionize"
> Reply: Philip Blood: "RE: limit on segment atom number in solvate and
> autoionize"
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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
>
>
>
>
>
>