VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Sep 23 2014 - 09:28:30 CDT

Hi Thierry,

NAMD doesn't specifically have resnames, as it doesn't have a force
field that goes with it. In fact, for many folks that use CHARMM as
their force field, CHARMM and NAMD have identical resnames. I think you
are getting confused by the pdb resnames, which tend to be less specific
than the force field resnames. For you examples, water in a crystal
structure is just H2O or HOH because they don't need to have parameters
associated with it. In simulations, there are dozens if not hundreds of
different water models (the most commonly used one with the CHARMM force
field is TIP3), so we usually alias our waters to TIP3 during structure
generation. Ditto for His. It can carry a proton on either the delta
(HSD) or epsilon (HSE) nitrogen or both (HSP). For a pdb structure it
doesn't matter, as the hydrogens can't really be observed directly
anyway in a crystal structure. But for atomistic force fields, the
choice of where that protonation sits can have real consequences on the
behavior of the simulation, so we need to make an explicit (and
informed) choice.

-Josh Vermaas

On 09/22/2014 10:58 PM, Thierry Oscar Wambo wrote:
>
> Hello everyone,
>
> does anyone knows if there is a file providing a list of equivalence
> between CHARMM and NAMD resname? (for example TIP3 <=> H2O; HIS <=>
> HSE and so on ....)
>
> Thank you!
>
>
> Thierry,
>
>
> UT San Antonio, TX
>
> Grad student
>
> Biophysics
>