VMD-L Mailing List

From: Manas Kohli (manaskohli1_at_gmail.com)
Date: Mon Feb 15 2021 - 08:51:54 CST

Dear Daniel,

Thank you for your email! I realised that the interaction energy is indeed
what I was after and after some more reading I realised I needed to adjust
the dielectric constant to get a more physiologically representative
result. My salt-bridge exists at the extracellular face of the protein i.e.
it faces water. Would you know of an appropriate dielectric constant to use
for this calculation? Thank you in advance!

Best wishes,
Manas

On Mon, Feb 15, 2021 at 1:23 AM Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
wrote:

> 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
>>
>