VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 05 2022 - 23:29:15 CDT

Hi,
  It shouldn't be necessary to run VMD as Administrator if file permissions
and your working directory are set appropriate when you're using plugins
that write output files in intermediate steps for launching NAMD or similar
apps. You should be able to check what environment variables you have set
in Windows (globally) that impact VMD. Both the 32-bit and 64-bit versions
pay attention to environment variables, so off the top of my head I don't
have an answer for why you'd get different behavior with respect to finding
NAMD automatically unless you have different path environment variables in
the two cases.

Best,
  John Stone
  

On Fri, Jun 17, 2022 at 11:22:28AM +0000, Efthymiou, Christos wrote:
> 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
> <[1]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 [2]https://github.com/HuiLiuCode/CaFE_Plugin 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.
>
> References
>
> Visible links
> 1. mailto:christos.dereschuk.20_at_ucl.ac.uk
> 2. 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$ 

-- 
Research Affiliate, 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/           
http://www.ks.uiuc.edu/Research/vmd/