VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 01 2021 - 00:38:32 CST

Hi,
  It would be great if you could actually provide enough details for
someone else to be able to try and reproduce the problems you're
describing. Obviously, nobody has intended to "disrupt" any features in VMD.

Since other users have not reported the issues you're describing,
it would be best if you could provide a set of input files and detailed
sequence of steps one can follow to recreate the problems you have encountered.

Often times the details are very important, and what you're describing below
in somewhat general sounding language may in fact only occur for the very
specific cases you're trying, in which case nobody would be able to guess
why you're having trouble without actually reproducing the problem
for themselves.

Without more detailed information, we can't hope to give you any
useful guidance or to find and fix software bugs that may exist.
>From the statements below, I can't even guess if you might be using
the tool incorrectly, there just isn't enough information.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 25, 2021 at 09:15:38AM +0100, Francesco Pietra wrote:
> Hello
> This is to ask which is the reason for disrupting some GUI features with
> VMD 1.9.4a55 linux.
> That is, in my hands, when dealing with organic molecules, Automatic PSF
> Builder requires deleting all Topology Files before adding those for the
> organic molecule, otherwise it does not work.
> With Add Solvation Box for non-acqueous, VMD crashes reporting errors,
> while psf/pdb are obtained correctly. VMD has to be restarted to measure
> center/cell dimensions
> I know that, to this regard, there are very useful tcl commands from the
> TK console, however with complex systems made of many chains - as it often
> occurs to me - the GUI relieves from much work
> thanks
> francesco pietra
> Beg pardon if all those problems simple arise from my incorrect use of the
> VMD GUI 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/