I have no AMBER 16 ... SO the ras-raf binding free energy in A3 tutorial is
reliable?
----- åå¤é®ä»¶ -----
å信人:Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de>
æ¶ä¿¡äºº:amber <amber.ambermd.org>
æ¶ é´:2017å¹´03æ24æ¥ 16æ¶51å58ç§
主 é¢:Re: [AMBER] åèªåå°è¹çé®ä»¶
Please use MMPBSA from Amber 16 ... Recently, we discovered a problem
with the calculation of the electrostatic energy in earlier versions of
Amber (see the thread "MMPBSA results with Amber 12 versus Amber 16"
from October 2016 in the mailing list archive)
It may be worth considering an alert about that issue in the MMPBSA
tutorials (as well as in the Amber Tools manuals) ...
Best
Vlad
On 03/24/2017 09:42 AM, 刘兰茹 wrote:
> Hello,
>
> I have a question about mmpbsa. I calculated binding free energy for
> ras-raf complex by Amber14, and the input files were downloaded from A3
> tutorial website. The results of binding free energy from PB calculated by
> Amber14 is about -28, which has a large difference compared with -86
> provided in the tutorial. But the results from GB are simliar. So my
> question is how to modify the parameters in AMBER14 so that I can get -86
> for binding free energy from PB ? I have attemped to add âuse _sander =
1â
> at .general , but no work.
>
> Thanksâ
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--
Vlad Cojocaru, Ph.D., Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Fri Mar 24 2017 - 03:00:02 PDT
