AMBER Archive (2004)

Subject: Re: AMBER: question about delphi and UHBD

From: Ray Luo (
Date: Tue Sep 28 2004 - 17:19:59 CDT

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.

Ray wrote:

>Yes. it's correct. Thank you Carlos.
>----- Original Message -----
>From: Carlos Simmerling <>
>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:
>> Brook, NY 11794-5115 E-

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:
Home page:

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