[AMBER] mdgx, improper terms and multifit

From: viktor drobot <linux776.gmail.com>
Date: Thu, 22 Aug 2019 20:23:06 +0300

Hello, community! I have two major questions related to mdgx.

*Question 1.* Is it possible to fit improper terms with mdgx? If not,
how should I properly handle them? If yes, what should I do in case if
there are dihedral term with the same naming exists (quite common for
big molecules)?

*Question 2.* Also I would like to clarify the following. Let's imagine
that we have two molecules, the second one is a derivative of the first
one - for example, quite large amine and its amide derivative. I've
already calculated quantum energies for both conformational libraries
and want to use both simultaneously during bonded parameter fit.
Although the most parts of both molecules are the same (hence
corresponding atom types), there are some differences - at least atom
type of acylated nitrogen in amide differs from atom type of amine and
also there are extra acyl part in amide exist.

So I want to know if it's possible to:
1) perform bonded parameter fit using two conformational libraries
(amine and amide) simultaneously
2) fit bonded terms from amine and amide, which are the same (actually
belongs to both molecules)
3) fit terms which involves amine/amide nitrogen (there will be
different atom types!)
4) fit terms from acyl part of amide
and do it within single config file for mdgx?

Actually I can't get how mdgx would proper handle the common nitrogen
for both molecules but of different atom type...

Any advices/help would be very appreciable. Thank you!

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Received on Thu Aug 22 2019 - 10:30:02 PDT
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