AMBER Archive (2009)

Subject: [AMBER] Unable to correctly identify element when running QM/MM in amber10

From: Jifeng Wang (wangjf_at_gmail.com)
Date: Thu Oct 22 2009 - 11:20:30 CDT

Hi, all,

I recompiled Amber10 recently after Bugfix1-22 was applied.

When I run QM/MM, it gave me an error msg like
"Unable to correctly identify element Zn".

I have a Zn atom in the QM region. So I assume it is because Zinc is not
recognized by sander (sander.MPI).

Then I went to bugfix 19, in which the following lines are added in
src/sander/qmmm_module.f (as many other lines):

+ elseif(atom_name(1:1) .eq. 'z' .or. atom_name(1:1) .eq. 'Z') then
+ if(atom_mass > 89.0d0 .and. atom_mass <= 93.0d0) then
+ atomic_number = 40 !Zirconium
+ else
+ write(6,*) 'Unable to correctly identify element ', atom_name
+ call mexit(6,1)
+ end if
+ else

So I added some additional lines for Zinc:

        elseif(atom_mass > 53.0d0 .and. atom_mass <= 83.0d0) then
          atomic_number = 30 ! Zinc
        else

Then, I recomplied amber. This time no error msg any more. I did not
really go though the code in
in qmmm_module.f. So I want to know if I've done this right?

Thank you.

-Jifeng
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