[AMBER] nonbonding parameters

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Wed, 23 Feb 2011 08:14:51 +0100

Hi all,

I have parametrized a new residue and needed to change the naming of
some of the atoms in the lib file so I am add the missing parameters.
I am not quite sure where to find the "nonbonding" interaction terms.
The residue I am trying to parametrize is a modified water molecule
and in the parm99.dat file I find the following parameters for TIP3P


  OW 1.7683 0.1520 TIP3P water model
  HW 0.0000 0.0000 TIP3P water model

What is the MOD4 and RE section?

The first part second column

PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
C 12.01 0.616 ! sp2 C carbonyl group
CA 12.01 0.360 sp2 C pure aromatic (benzene)

what does the second column mean?


AMBER mailing list
Received on Tue Feb 22 2011 - 23:30:05 PST
Custom Search