VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Sep 22 2014 - 23:50:14 CDT

Hi,

As far as I know there is no equivalence.

Histidine has two states at pH 7.0 it could be carrying a charge at and the
Delta or Epsilon carbon - leading to the name HSD or HSE.

Water has different models. Most popular (I use) is the 3-point model. It
is written as TIP3P (the residue name).

Water under charmm or namd is always treated as TIP3P.

The main question is how the force field recognizes the residues as, which
bring us to the point - what exactly is it that you are trying to do. Why
would you want to rename TIP3P to H2O ?

In pdb files we always have HIS - (the state is not assigned) some programs
(and by this I mean ways of taking preprocessing a system -making psf/
adding hydrogens) warn about this - other automatically substitute HIS with
HSD (which may not always be the case) ... a little more info maybe
necessary before an answer can given !!

Best,
/A

On Tue, Sep 23, 2014 at 3:58 PM, Thierry Oscar Wambo <Thierry.Wambo_at_utsa.edu
> 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
> 

-- 
Best,
/A