VMD-L Mailing List

From: Thierry Oscar Wambo (Thierry.Wambo_at_utsa.edu)
Date: Tue Sep 23 2014 - 10:57:53 CDT

Thanks for all your explanations!

I was doing a phosphorylation and the psfgen didn't directly recognize HOH and I had to aliase it as TIP3. Now based on your responses I understand why.

Regards,

Thierry

________________________________
From: Josh Vermaas <vermaas2_at_illinois.edu>
Sent: Tuesday, September 23, 2014 9:28 AM
To: Thierry Oscar Wambo; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Resname CHARMM to NAMD

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