Re: [AMBER] What if MM Energy > QM Energy Even Vn=0

From: David A Case <>
Date: Sat, 4 Dec 2021 11:40:35 -0500

On Sat, Dec 04, 2021, Erdem Yeler wrote:

>I am trying to parameterize a metal dihedral. I tried to parameterize this
>dihedral by using mdgx and/or paramfit but I couldn't achieve it. Then I
>wrote a script for this but also this script failed (even if it worked
>perfectly for other dihedrals), I changed the molecule design (used similar
>molecules) and tried again and again but I got nothing. Here is the
>problem: Me is a metal atom and for "os-Me-ca-ca" dihedral MM relative
>energy is greater than QM energy even if I put in frcmod file this:
>os-Me-ca-ca 1 0.000 0.000 0.000
>NOTE: bond and angle parameters are almost OK. There was no imaginer peak
>in FTIR but The metal is transition metal and VFFDT calculate some
>Me-os bonds as 0.000kcal/mol.
>Here is the chart when I use Vn=0:
>How can I solve this problem?

I'm guessing that for the MM curve, you are seeing the change in non-bonded
interactions (and not the change in dihedral energy) as you rotate about the
Me-ca bond. (This assumes that your frcmod file is being correctly read,
etc.) If so, look at the a configuration near the top of the MM curve, and
see if you can spot clashes or other interactions that would lead to a
higher energy than QM is predicting.

Others might have more relevant experience or suggestions here....


AMBER mailing list
Received on Sat Dec 04 2021 - 09:00:02 PST
Custom Search