Re: AMBER: AMBER 9 - Force Field Options - Question

From: WANG,YING <>
Date: Wed, 17 Oct 2007 11:47:05 -0400 (EDT)

Hi, Dear all, I also have some question about the forcefield
selection and would like to get some help from you..........

1. Now I do simulation of a protein and try to unfold it, I use
ff03 (duan) forcefiled. The result is fine until now. Next step I
try to bind it with a carbonhydrate and then do simulation of this
glyco-protein. I know that I should choose glycamxx forcefiled to
deal with the sugar part, but I would like to know is it fine to
combine the glycamxx with the ff03 (Duan) forcefiled in a system?
Sorry for this stupid question........

2. I also try to do simulation of a linear poly carboxylic acid,
could you tell me which force filed I can use? I saw the parm91 is
for general organic molecules. Is it too old? The gaff is new but
I saw the comments said that it might have problem to deal with
some molecules. So I'm confused.............

Could anybody give me some suggestion? Or some reference
literature? It will be greatly appreciated............

Have a good day!


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Oct 21 2007 - 06:07:10 PDT
Custom Search