From: Manas Kohli (
Date: Mon Feb 15 2021 - 13:02:25 CST

Dear Peter,

Thank you for your response. If I were to do free energy calculations, how
would I go about doing them for intramolecular salt-bridges i.e. between
two amino acids in the same transmembrane protein? So far I got links for
looking at binding free energy between a ligand and protein but I don't
think that's what I'm after. Any help would be really appreciated.

Thanks and Best Regards,

On Mon, Feb 15, 2021 at 5:07 PM Peter Freddolino <> wrote:

> Hi Manas,
> I think it is really important for us to know what your end goal is for
> this calculation. What energy are you really looking for? NAMDenergy is
> giving you the actual nonbonded energy (Coulomb + LJ) of the interacting
> groups in the force field of your calculation. If you're looking for
> something like the contribution of a salt bridge to the stability of a
> particular confirmation, or inter-molecular complex, you need to be getting
> into the world of free energy calculations. This is beyond what namdenergy
> provides. Just coming up with an ad hoc dielectric constant is unlikely to
> help the situation.
> Best,
> Peter
> On Mon, Feb 15, 2021 at 10:38 AM Manas Kohli <>
> wrote:
>> 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 <>
>> 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 <>
>>> 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