VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Sun Feb 14 2021 - 19:23:10 CST

That seems about right, what's the issue?

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Mon, Feb 15, 2021 at 2:56 AM Manas Kohli <manaskohli1_at_gmail.com> wrote:

> 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
>