Hello,
I noticed that there was an article about QwikMD which makes running the NAMD simulations easier, complex, and efficient.
But I have a problem. I'm just doing the basic example where I have to rename a protein, and I have to import the topology file to rename the the atoms in the protein, basically C becomes C1, so forth.
But the issue is that permission is denied in /usr/local/lib/ ...
Error:
"couldn't open "/usr/local/lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all36_cgenff.rtf": permission denied
couldn't open "/usr/local/lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all36_cgenff.rtf": permission denied"
Normally if I have an issue with permission denied, I run the program as root in linux or just sudo. But I can't launch vmd as root. Then again, this error doesn't make any sense because I installed vmd in a subfolder of /usr/local/lib which is the same place where I can't open the vmd topology files to edit!?
What do you think I should do?
I appreciate your help with this troubleshooting.
-Adron
Perhaps the permissions to vmd subfolders have been messed up? Try recusrsive chmod and chown. In your case something like:
- sudo chmod -R 644 /usr/local/lib/vmd/plugins
- sudo chown -R user:user /usr/local/lib/vmd/plugins (where user is your username)
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