Re: Problem with namd 2.13 constant pH molecular dynamics, HSD residue.

From: Brian Radak (
Date: Fri Apr 19 2019 - 08:33:04 CDT

That is weird - the newest version of the code and protein force field
should automatically alias HSD, HSE, and HSP as HIS. the change from older
versions is that the alias info is in the json file rather than being
hard-coded (which might explain the discrepancy).

Can you send me your json file offline? Alternatively, try re-downloading
the json files from the tutorial (in future releases these will just ship
with NAMD) and try again.


On Fri, Apr 19, 2019, 9:03 AM Ingrid Bernardes Santana Martins <> wrote:

> Hello!
> I want to run a Constant pH molecular dynamics with namd 2.13 and I have
> histidins in my system, named HSD on my pdb and psf. The namd didn't
> understand it as a titrable residue. But, I did it before with namd 2.12
> and it worked fine. Someone knows what should I do? If just rename the pdb
> and psf to HIS instead of HSD is enough and correct?
> Thanks!

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