Re: [AMBER] QM/MM/MD g09 interface issues,

From: Fabrício Bracht <>
Date: Thu, 8 Dec 2016 14:46:25 -0200

Hi David. Have you tried using parmed to correct the atomic number of the
zinc atom. I had a similar problem and there seems to be a problem
regarding that. I am not sure if it happens just for zinc or if it is
system specific.
In parmed you type
printdetails mask (mask being the zinc atom id)
See if the At.# column has the correct atomic number for zinc.
Even if it says 30, try typing
change ATOMIC_NUMBER mask 30 (again mask you have to change for your system)
Probably you will see something like "ATOMIC_NUMBER changed from -1 to 30".

I have had this problem multiple times and sometimes , even when the At.#
says 30 (for zinc), it is not 30.

Hope it helps

2016-12-08 14:01 GMT-02:00 David Poole <>:

> Hello everybody,
> I am using amber15 to interface with g09 to do some exciting qm/md
> with a metal center. However, when the interface goes to write atomic
> symbols, it replaces my zinc with '^@^@', and unfortunately Gaussian
> doesn't quite get emoticons.
> Hence, I gotta ask, what's up and if there is an easy fix for it.
> I think the line in question is:
> write(iunit,'(a2,1x,3f25.16)') elementSymbol(qmtypes(i)),
> qmcoords(1:3,i)
> Which gets back to the 'element_orbital_index' included, but I've not
> found that yet.
> Thank ye kindly,
> -David
> oh, also, this is a pretty dumb question but how do I reply on a
> thread topic? or get individual replies to my conversation, I can't
> seem to find settings for the mailing list control or generally how to
> use it well.
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Received on Thu Dec 08 2016 - 09:00:03 PST
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