[AMBER] mm_pbsa and MMPBSA.py

From: <zmatovic.kg.ac.rs>
Date: Thu, 28 Oct 2021 15:57:15 +0200

Dear Amber friends,

I used again to check my perception about deltaG determination across MMPBSA
(tutorial http://ambermd.org/tutorials/advanced/tutorial3). Namely, some
inconsistency appear between ras_raf and estrogen_raloxifen cases. In the
first case (using both ways mm_pbsa.pl and MMPBSA.py) the total system
ras_raf is neutral so there is no need for adding counterions after
solvations (both methods). However, in case of estrogen_raloxifen
solvated 1err.solvated.prmtop parameter file charge the unit with -7 so as
the complex.prmtop and receptor.prmtop files. So I wonder is this
postprocessing (after production) treatment or something else..? Does it
mean we shouldn't have any ion within solvated, complex_dry, receptor and
ligand files? May be this is already explained in some already posted quests
in this group and if so I am excusing myself and ask kindly to direct me to
that post.


I wish you all to have a very nice day.







A true friend is someone who is there for you

when he'd rather be anywhere else.

-- Len Wein


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Received on Thu Oct 28 2021 - 07:00:02 PDT
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