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

From: WANG,YING <>
Date: Wed, 17 Oct 2007 15:11:19 -0400 (EDT)

Hi, Thanks very much!!
Could I ask the first Q further? Do you mean that for large
molecules using to get the charge? When I use 03ff to
simulate the protein, I use, is it that
DFT/cc-pvtz(pcm=ether) charges you mentioned about? And for the
sugar part I try to use glycamxx, is it right?

And there is fewer records in parm99 and parm94 than in parm91.
For example, in parm91, there is a bond paramter: C -C2 317.
1.522 for GLY,ASP,GLU. And the gaff define that C2 is Sp2 C.
But in parm99, it doesn't have this C -C2 term, moreover, it
doesn't have C2, C3... atom definition. Could you kindly tell me
which symbol it use to represent these atoms? Thanks very much!!
Sorry to interrupt you!!


On Wed Oct 17 12:25:16 EDT 2007, Yong Duan <>

> 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: [] On
> Behalf Of
> Sent: Wednesday, October 17, 2007 8:47 AM
> To:
> 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 - 06:07:13 PDT
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