[AMBER] gaff with and without gaff atom types

From: Erdem Yeler <erdemyeler.gmail.com>
Date: Sun, 5 Jan 2020 19:32:08 +0300

I parameterized some novel molecules for AMBER but it is very strange that
when I use gaff atom types in the mol2 and frcmod file, minimized geometry
moves away from the real X-ray structure... but when I use with the
--almost-- same parameters with the AMBER Atom type (you know, ouput from
parmchk2 without any flag, capital letters frcmod file) I am getting really
good results.
Here is example:
M is the non-standard atom

when I use this file with gaff (I shortened the file of course. in my real
frcmod all parameters are avaliable):

M -os-c3 112.86 222.210 seminaro
oh-M -os 100.85 141.940 seminaro
os-M -os 88.101 216.130 seminaro
M -oh-ho 45.820 114.920 seminaro
x - x -x 122.222 222.2 same as x-x-x

my results are terrible. Minimized geometry and X-ray structure are totally
different. but when I use this:

parmchk2 -i MMMM.mol2 -f mol2 -o MMM_nitrur.dat

and then when I fill the dat file's ATTN lines manually

M -O -C 112.86 222.210 vffdt results
O -M -O 100.85 141.940 vffdt results
M -O -O 45.820 114.920 vffdt results
X- X -X 122.222 222.2 same as X-X-X
I am getting wonderful results. You can say oh-M -os and os-M -os are both
can be expressed as O -M -O in the second file, but I cheked it and changed
these "common parameters" and I got the same results. My question is: What
is the reason for that? How can I get the same results from 2 different
Thank you
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Received on Sun Jan 05 2020 - 09:00:02 PST
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