VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 16 2022 - 09:39:35 CDT

Hi,
  Indeed, that sort of an error sounds like a script/plugin making assumptions
about the current working directory vs. where the file is actually located.
It's best to ensure that you've got your current working directory set
to the place where the files you're going to be reading/writing are
located. That avoids issues when using scripts that aren't very
sophisticated in their handling of fully-qualified paths.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 16, 2022 at 07:32:12PM +0800, Ashar Malik wrote:
> My experience with this kind of error (for general work not related to
> CaFE) was in 2014 when we had VMD running on Windows machines in the
> labs.Â
> This was overcome by running vmd in administrator mode or changing the
> working path to a location where you have read/write access.Â
> Hope this helps.Â
> On Thu, Jun 16, 2022 at 7:13 PM Efthymiou, Christos
> <[1]christos.dereschuk.20_at_ucl.ac.uk> wrote:
>
> Hello,Â
> I have run some molecular dynamics simulations on a protein-protein
> complex and I would like to use the CaFE VMD plugin to calculate the
> free binding energy of this association. I am using a Windows 10
> computer and have both the 32bit and 64bit versions of VMD available. I
> downloaded the code from github
> here [2]https://github.com/HuiLiuCode/CaFE_Plugin and followed the
> manual to set everything up for the program to work within VMD.Â
> The first problem I experience is when I try to run the program
> according to the command given in the manual. To run the program, the
> manual says to use the commandÂ
> vmd -dispdev text -eofexit < script.vmd > vmd.logÂ
> When I try to run that command, I get the following error:Â
> couldn't write file "vmd.log": permission deniedÂ
> In any case, when I instead use the standard command of source
> script.vmd, the program runs and prints the following:Â
> CaFE) Sanity checkÂ
> CaFE) Found 5508 atoms for complexÂ
> CaFE) Found 4646 atoms for receptorÂ
> CaFE) Found 862 atoms for ligandÂ
> CaFE) Loaded 10000 frames for complexÂ
> CaFE) Generating new trajectory for complexÂ
> Unable to load file '_mmpbsa_com_tmp.dcd' using file type 'dcd'.Â
> I am not sure what the _mmpbsaâ**_com_tmp.dcd file is, or why the
> program is unable to open it. Please let me know if you have any
> solution to this problem as I really would like to be able to use this
> program for calculating free binding energy.Â
>
> References
>
> Visible links
> 1. mailto:christos.dereschuk.20_at_ucl.ac.uk
> 2. https://urldefense.com/v3/__https://github.com/HuiLiuCode/CaFE_Plugin__;!!DZ3fjg!9LoRkGcxHvksd5uLW4u9TVC-fA9Gj9AFrrG3yLGGzwqTQIoFIM3k4dGhitEHEKgrjRtQRshQfRlYP-_vS77qzCk2p8yinLs$ 

-- 
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/