VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Wed May 24 2023 - 11:09:20 CDT

Hi Janni,

Sorry for the lack of reply to your question! Did you have any luck in resolving the issue? Are you using the latest version of VMD and BFEE? Regardless, there’s also a stand-alone version now: https://urldefense.com/v3/__https://github.com/fhh2626/BFEE2__;!!DZ3fjg!79Fyzzam20wsAPjAT9gnFsAlVYJOnpJK7E7vNafCqFU8r5lgA7xUr-aQDdvfZDB6bkRzxEa2UV_e79ee2YvkSKfj_Q8$

Best,
JC

On May 9, 2023, at 3:03 AM, Janni Christensen <jac_at_expres2ionbio.com<mailto:jac_at_expres2ionbio.com>> wrote:

Hi all,
I am trying to use the BFEE plugin in VMD to calculate the free energy of a protein-ligand complex. However, I keep getting the error below when I try to generate the input files.
"Unable to load file 'C:/PATH/File.coor' using file type 'namdbin'."
I cannot find any place when the file type can be changed if that is the issue.
I do not get any errors when I type "mol addfile type namdbin File.coor" in the TkConsole. Still BFEE won't accept my MD equilibration run files.
Any help is greatly appreciated.

Med venlig hilsen / Best regards

Janni Christensen, PhD
Downstream Development Scientist
ExpreS2ion Biotechnologies
Agern Allé 1, DK-2970 Hørsholm, Denmark<https://urldefense.com/v3/__https://goo.gl/maps/TgGLEBz8uGrmfuLPA__;!!DZ3fjg!9lam2RYlUOk8SjXp3-4D7TEmeVYEXYV31uEJgg_INK6g1ZEG9ddldjl0cx3Q5dBIHsIQ46UVqFR9IIBLLQ$>
jac_at_expres2ionbio.com<mailto:jac_at_expres2ionbio.com>