AMBER Archive (2009)
Subject: RE: [AMBER] Unable to correctly identify element when running QM/MM in amber10
From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Oct 22 2009 - 14:03:40 CDT
You are correct. I must have forgotten Zinc when I made the bugfix. What you
added should work fine, if you use a Hamiltonian which does not have
parameters for zinc the code will quit elsewhere so you do not need to
worry. I will make an additional bugfix to add support for Zinc.
All the best
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Jifeng Wang
> Sent: Thursday, October 22, 2009 9:21 AM
> To: amber_at_ambermd.org
> Subject: [AMBER] Unable to correctly identify element when running
> QM/MM in amber10
> 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
> 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')
> + if(atom_mass > 89.0d0 .and. atom_mass <= 93.0d0) then
> + atomic_number = 40 !Zirconium
> + else
> + write(6,*) 'Unable to correctly identify element ',
> + 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
> 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.
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