Re: [AMBER] QM/MM issue with boron containing compound (AMBER16)

From: David A Case <>
Date: Thu, 10 May 2018 14:48:01 -0400

On Thu, May 10, 2018, Bodee Nutho wrote:
> I'm trying to perform QM/MM MD on a boron-containing compound.
> I did perform an equilibration of the complex for 1-ns using classical MD
> simulation. Everything seems to be fine with this classical MD.
> After that, I switched from running classical MD to QM/MM MD using PM6
> Hamiltonian. I have found the problem with the reading of boron atom in
> which boron atom turned to be an unknown element.
> How should I solve this problem?

Can you examine your prmtop file (either with parmed or just with a text
editor): what is the atom name for atom 2413? Easiest to do would be
run parmed, and issue the command "printDetails .2413": see if the name,
mass, atomic number, etc. are correct.

The underlying problem is probably in how you made the prmtop file in
the first place, perhaps lacking an "AddAtomType" command in leap. MM
calculations don't really care about the atomic number, but QM
calculations do. Probably just editing the ATOMIC_NUMBER section of the
prmtop file to provide the proper atomic number will help.

...good luck....dac

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Received on Thu May 10 2018 - 12:00:01 PDT
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