VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Thu Jun 16 2022 - 05:30:17 CDT

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!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.