AMBER Archive (2007)

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

From: WANG,YING (wangying_at_ufl.edu)
Date: Wed Oct 17 2007 - 14:11:19 CDT

Hi, Thanks very much!!
Could I ask the first Q further? Do you mean that for large
molecules using all_xx94.in to get the charge? When I use 03ff to
simulate the protein, I use all_amino03.in, 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!!

Ying

On Wed Oct 17 12:25:16 EDT 2007, Yong Duan <duan_at_ucdavis.edu>
wrote:

>
> 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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
> Behalf Of
> WANG,YING
> Sent: Wednesday, October 17, 2007 8:47 AM
> To: amber_at_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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> 

--
WANG,YING
Mechanical and Aerospace Engineering
University of Florida
Office: NEB 139
TEL: 001-352-846-3030

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu