Re: How do NTC=2 recognize hydrogen atom?

From: David A. Case <>
Date: Thu, 20 Feb 2003 08:19:27 -0800

On Wed, Feb 19, 2003, yuan bo wrote:

> It is know that NTC=2 constrain bonds containing
> hydrogen in MD simulation. I have one problem: How do
> Amber recognize the hydrogen atom in MD simulation, by
> atom type name( i.e the first letter in type name is
> "H" ) or other characters?

This is done in LEaP, with the element code in the addAtomTypes command: see
leaprc.ff94 (or related files). If the second entry for an atom type is
"H", it is hydrogen....Leap doesn't care what the first character of the
atom name is.

So you could probably use this feature to "trick" Amber into thinking that
an atom named "X" is a hydrogen. But please be careful, and check your
prmtop output to be sure that bonds to "X" are really be classified as

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Thu Feb 20 2003 - 16:53:01 PST
Custom Search