AMBER Archive (2004)

Subject: Re: AMBER: question about delphi and UHBD

From: xhu1_at_memphis.edu
Date: Wed Sep 29 2004 - 14:11:47 CDT

Thank you, Ray. I will try this too.

----- Original Message -----
From: "Ray Luo" <rluo_at_uci.edu>
Date: Tuesday, September 28, 2004 4:19 pm
Subject: Re: AMBER: question about delphi and UHBD

> Another possibility is that UHBD, by default, does not assign
> protein
> dielectric according to "molecular surface", but according to "van
> der
> Waals surface". However, in Delphi, there is only the choice of
> "molecular surface". The difference in solvation energies can be
> huge
> when different surfaces are used.
>
> Best,
> Ray
>
> xhu1_at_memphis.edu wrote:
>
> >Yes. it's correct. Thank you Carlos.
> >
> >Shawn
> >
> >----- Original Message -----
> >From: Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>
> >Date: Tuesday, September 28, 2004 2:46 pm
> >Subject: Re: AMBER: question about delphi and UHBD
> >
> >
> >
> >>did Delphi correctly read your charges? look at the output file
> >>to make sure.
> >>
> >>===================================================================
> >>Carlos L. Simmerling, Ph.D.
>
> >>Associate Professor Phone: (631) 632-1336
> >>Center for Structural Biology Fax: (631) 632-1555
> >>Stony Brook University Web:
> >>http://comp.chem.sunysb.edu/carlosStony Brook, NY 11794-5115
> E-
> >>mail: carlos.simmerling_at_stonybrook.edu
> >>===================================================================
> >>
> >>
> >>
>
>
> --
> ====================================================
> Ray Luo, Ph.D.
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
> Office: (949)824-9528 Lab: (949)824-9562
> Fax: (949)824-8551 e-mail: rluo_at_uci.edu
> Home page: http://rayl0.bio.uci.edu/rayl/
> ====================================================
>
>
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