VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Fri Nov 20 2009 - 12:09:51 CST

Francesco,

Where did you get the cgsolvate.tcl file from? Are these from the
http://www.ks.uiuc.edu/Research/CG/rbcg/files/ directory? If so, I looked at
the cgsolvate.tcl file there, and it looks like it is probably a revision of an
old version of solvate. I don't know what Anton has told you about the file,
but I suspect that it worked at one point with an earlier version of VMD (and
solvate) but needs to be updated to be current. I haven't compared the two
line-by-line, though, so I can't say for sure.

Kirby

Francesco Pietra wrote:
> Hi:
>
> In order to water solvate a cg protein (cg pdb abd psf available) with
> VMD1.8.7 I am following Anton's advice to solvate with gc water
> instead of cg an "all-atom protein water system", using the files that
> Anton has put on the web:
>
> cgsolvate.tcl
> cgwat.pdb
> cgwat.psf
>
> I tried to use cgsolvate.tcl in place of solvate.tcl. If cgsolvate.tcl
> is added to
>
> /usr/local/lib/vmd/plugins/noarch/tcl/solvate1.3
>
> it is not seen by the command
>
> package require ...
>
> Then I put cgsolvate.tcl in my working directory. Command
>
> source cgsolvate.tcl
>
> reported
>
> conflicting versions provided for package "solvate": 1.3, then 1.2.
>
>
>
> I would appreciate very much instructions. Thanks
>
> francesco pietra 

-- 
Kirby Vandivort                      Theoretical and
Senior Research Programmer            Computational Biophysics
Email: kvandivo_at_ks.uiuc.edu          3061 Beckman Institute
http://www.ks.uiuc.edu/~kvandivo/    University of Illinois
Phone: (217) 244-1928                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA