VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Fri Jun 17 2022 - 06:22:28 CDT

Thank you for the advice! Running VMD in administrator mode seems to fix the previous problem, but now I am having trouble with VMD recognizing namd. I get the following error:

````
(VMD) 12 % source CaFE_Script.vmd
CaFE) Sanity check
CaFE) Found 5508 atoms for complex
CaFE) Found 4646 atoms for receptor
CaFE) Found 862 atoms for ligand
CaFE) Loaded 8411 frames for complex
CaFE) Generating new trajectory for complex
CaFE) Loaded 9 frames for complex
CaFE) It took 0 days 0 hrs 12 min 37 sec
CaFE) Calculating the MM term
couldn't execute "namd2": no such file or directory
````
I just recently downloaded the 64bit version of VMD which is what I am using for this plugin, but I originally downloaded the 32bit VMD 1.9.3 and NAMD together, and that still seems to work. How do I make the latest version of VMD recognize that namd is on my computer? I can't recall how I made it work previously for the 32bit version of VMD.

Thank you again for all the help.
________________________________
From: Jason Smith <jason_smith_18_at_sfu.ca>
Sent: Thursday, June 16, 2022 4:50 PM
To: Ashar Malik <asharjm_at_gmail.com>; Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Error with CaFE VMD Plugin

⚠ Caution: External sender

My Experience with VMD in general (not having used CaFE specifically) is that this is indeed a common problem on windows not having file permissions in the default c:\whatever locations. With science programs in general, I be sure to look for things like all read/write operations occurring in a location I have all permissions for, running in administrator mode if necessary/possible, and checking whether the program is attempting to run in UAC mode.

Cheers,

-
Jason Smith
Post-Doctoral Fellow
Robert N. Young Lab, Simon Fraser University
8888 University Drive, Burnaby, BC, V5A-1S6
Canada

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Ashar Malik <asharjm_at_gmail.com>
Sent: Thursday, 16 June 2022 4:32:12 AM
To: Efthymiou, Christos
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Error with CaFE VMD Plugin

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<mailto: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!_vWE2TtYqsXfpxYZC3XsEtuRGNfRM06oqME2rhMuhcHDuwzqwid29HoXjmHG0AkgOTVcBa8a0p_m5oIvBoiM16yvb5DLg1Y$ <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fgithub.com*2FHuiLiuCode*2FCaFE_Plugin__*3B!!DZ3fjg!9LoRkGcxHvksd5uLW4u9TVC-fA9Gj9AFrrG3yLGGzwqTQIoFIM3k4dGhitEHEKgrjRtQRshQfRlYP-_vS77qzCk2p8yinLs*24&data=05*7C01*7Cchristos.dereschuk.20*40ucl.ac.uk*7C4a0fde028f4e4c599cc508da4fafe344*7C1faf88fea9984c5b93c9210a11d9a5c2*7C0*7C0*7C637909914121737506*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=VdAnijih1j*2FmvaYuP8s8HG9B9kEjHojcPMGq8KQXprQ*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!_vWE2TtYqsXfpxYZC3XsEtuRGNfRM06oqME2rhMuhcHDuwzqwid29HoXjmHG0AkgOTVcBa8a0p_m5oIvBoiM16yvcqBw-wI$ > 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.