VMD-L Mailing List

From: Manas Kohli (manaskohli1_at_gmail.com)
Date: Sun Feb 14 2021 - 07:54:51 CST

Hi all,

I'm trying to calculate the free energy between two residues in a
salt-bridge in my protein structure. I used the NAMD energy plugin and for
input I specified protein and resid x and similarly protein and resid y for
the two residues to select for. According to the NAMD energy documentation,
the output should be in kcal/mol but I seem to be getting values in the
range -100kcal/mol for an individual salt-bridge energy calculation. Am I
doing something wrong in the calculation phase or specifying the wrong
input? I know it may be difficult to troubleshoot the problem without
seeing the structure but if anyone has a general idea, I'd appreciate it
and can attach sample pdbs and similar information in subsequent emails if
that helps.

Thanks and Best Regards,
Manas