AMBER Archive (2007)

Subject: RE: AMBER: question about h bond

From: WANG,YING (wangying_at_ufl.edu)
Date: Fri Oct 19 2007 - 23:07:49 CDT

Hi, Thanks very much for your nice reply!!

Could I ask more about the electrostatic interaction? I saw the
expression of the potential terms, if I only use coulumb sum to
calculate the electrostatic interaction, is it enough? Because I
do the simulation of a non-periodic systerm so I cannot apply PME
methods.

BTW: And could you kindly tell me where I can find the vdw
parameters in parm99?

Thanks very much!!

On Fri Oct 19 20:41:19 EDT 2007, Yong Duan <duan_at_ucdavis.edu>
wrote:

>
> Explicit hydrogen bond terms using the (traditional) 10-12
> formula was
> present in earlier AMBER force fields. In more recent force
> fields, the
> hydrogen bonds are effectively modeled by the electrostatic
> interactions.
> Therefore, there are no longer explicit 10-12 terms in the new
> force fields.
> Hope this helps.
>
> yong
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
> Behalf Of
> WANG,YING
> Sent: Friday, October 19, 2007 5:20 PM
> To: amber_at_scripps.edu
> Subject: AMBER: question about h bond
>
>
> Hi dear all,
> I have a question about hydrogen bonds parameters of amber 9. I
> check the force files, and found that parm 91 has h bonds
> parameters but I didn't find it at other forcefield files like
> parm99. I use another software to do the simulation by using
> amber forcefiled so I have to modified the format of the
> forcefiled file and check all the forcefiled parameters. Could
> anybody tell me where I can find it? Or amber just use the h bond
> parameters of parm91.dat? Thanks very much!!
>
>
> --
> WANG,YING
>
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--
WANG,YING
Mechanical and Aerospace Engineering
University of Florida
Office: NEB 139
TEL: 001-352-846-3030

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