Did you change the mass of the Zn element? If you have AmberTools 12, what
is the output of:
parmed.py your.prmtop << EOF
printDetails .Zn
EOF
(In this case, your.prmtop is the prmtop of your system and Zn is the atom
name of your Zinc atom). This should print out the mass. Since atomic
numbers in QM/MM calculations are currently determined by mass, a bad
atomic mass may result in this error. Specifically, a Zinc atom is
recognized if the first letter of the atom name is "Z" and the atomic mass
is between 61 and 69.
HTH,
Jason
On Wed, Jan 9, 2013 at 4:55 PM, Agnieszka Dybala-Defratyka <
agnieszka.dybala-defratyka.p.lodz.pl> wrote:
>
> Dear Amber developers and users,
>
> I am working with a protein system containing zinc ion complex in its
> active site. I want to include it in the QM part of the system during QM/MM
> calculations but unfortunately neither PM3 nor PM6 allows for correct
> identification of this element.
> I am using Amber11 and all attempts to run QM/MM minimization failed with
> the following error message:
> 'Unable to correctly identify element Zn'
> I have tried to follow the similar posts in the Archive but all of them
> were related to Amber10 and it has been fixed since then, so I am wondering
> what could be wrong. I have checked qmmm_module.f file in the distribution
> I have and the lines for Zn are there.
>
> Thank you in advance,
> Agnieszka
>
>
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jan 10 2013 - 06:30:03 PST
