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

From: Yong Duan <duan.ucdavis.edu>
Date: Wed, 17 Oct 2007 09:25:16 -0700

Simple answer to your first Q is yes. We actually do that too. FYI, for
large molecules we often derive charges using parm94 approach. For small
molecules and amino acids, we prefer DFT/cc-pvtz(pcm=ether) charges.

To your second Q, every ff has some problems if you dig further, given the
nature of the ff development. The question is really which one is better.
Between parm91 and gaff, my impression is that gaff is a notable
improvement.


yong

-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
WANG,YING
Sent: Wednesday, October 17, 2007 8:47 AM
To: amber.scripps.edu
Subject: Re: AMBER: AMBER 9 - Force Field Options - Question


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!

Ying

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Received on Sun Oct 21 2007 - 06:07:10 PDT
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