Le Monday 13 May 2019 à 06:40:57PM, Thomas Gaillard a écrit :
> Dear AMBER developers,
>
> Comparing MMPBSA results with radiopt option set to 0 or 1, I obtain
> different values for the dispersion term (and of course for the PB term,
> but the same value for the cavity term). Is this expected?
>
> This was already mentioned
> (http://archive.ambermd.org/201702/0421.html).
>
> I was thinking that radiopt=1 would only affect the PB radii, not the
> radii used for the cavity and dispersion terms.
>
> Thanks for your time,
Hi,
I am adding an example to illustrate my question.
This is the PB test of MMPBSA.py
(AmberTools/test/mmpbsa_py/02_Poisson_Boltzmann) with radiopt set to 0
or 1:
MMPBSADI radiopt=0
&general
startframe=1, endframe=2, interval=1,
keep_files=0, debug_printlevel=2
/
&pb
istrng=0.1, inp=2, radiopt=[01],
/
Only the receptor energies are reported.
radiopt=0:
EPB -3255.0199
EDISPER -1134.8265
radiopt=1:
EPB -3188.8747
EDISPER -1128.0331
Other terms (VDWAALS, EEL, ENPOLAR) are identical.
I recall my question: is it expected that the EDISPER term is affected
by radiopt?
I can make other tests if it can help.
Thanks,
--
Thomas Gaillard
Professeur assistant
Laboratoire de Biochimie
Ecole Polytechnique
91128 Palaiseau cedex
tel: +33 1 69 33 48 62
fax: +33 1 69 33 49 09
thomas.gaillard.polytechnique.edu
http://thomasgaillard.fr
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Received on Tue Jun 11 2019 - 07:00:05 PDT
