VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Jun 16 2022 - 06:32:12 CDT

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.

This was overcome by running vmd in administrator mode or changing the
working path to a location where you have read/write access.

Hope this helps.

On Thu, Jun 16, 2022 at 7:13 PM Efthymiou, Christos <
christos.dereschuk.20_at_ucl.ac.uk> wrote:

> Hello,
>
> 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 https://urldefense.com/v3/__https://github.com/HuiLiuCode/CaFE_Plugin__;!!DZ3fjg!5EgsSqPucVMzV51ARjhaeIZGVpYctrZoT4GqJ8giWT4DkJclT10Z7sfMy7Igjeoe4Z4HiW6cK6vfkiTt$
> <https://urldefense.com/v3/__https://github.com/HuiLiuCode/CaFE_Plugin__;!!DZ3fjg!9LoRkGcxHvksd5uLW4u9TVC-fA9Gj9AFrrG3yLGGzwqTQIoFIM3k4dGhitEHEKgrjRtQRshQfRlYP-_vS77qzCk2p8yinLs$> and
> followed the manual to set everything up for the program to work within
> VMD.
>
> 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 command
>
> vmd -dispdev text -eofexit < script.vmd > vmd.log
>
> When I try to run that command, I get the following error:
>
> couldn't write file "vmd.log": permission denied
>
> In any case, when I instead use the standard command of source script.vmd,
> the program runs and prints the following:
>
> CaFE) Sanity check
> CaFE) Found 5508 atoms for complex
> CaFE) Found 4646 atoms for receptor
> CaFE) Found 862 atoms for ligand
> CaFE) Loaded 10000 frames for complex
> CaFE) Generating new trajectory for complex
> Unable to load file '_mmpbsa_com_tmp.dcd' using file type 'dcd'.
>
> I am not sure what the _mmpbsa​_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.
>
>