[AMBER] Zn protease

From: Hector A. Baldoni via AMBER <amber.ambermd.org>
Date: Tue, 18 Jul 2023 18:29:59 -0300

Dear Amber developers,

I have run and successfully completed eight dynamics of carbonic
anhydrases with pmemd.cuda and sander.MPI.
The zinc of the catalytic site was defined with the model proposed by
Pang YP
(https://www.mayo.edu/research/labs/computer-aided-molecular-design/projects/zinc-protein-simulations-using-cationic-dummy
-atom-each-approach).
A problem arises when trying to refine the dynamics using QM/MM
(sander+quick).
a) If I include the Zinc atom in the quantum region, the geometric
minimization continues without problem.
b) if the zinc atom is not included in the quantum region, the geometric
minimization aborts with the following message:

--------------------------------------------------
    3.1 QM CALCULATION INFO
--------------------------------------------------
Unable to correctly identify element Zn
Note: element guessing does not work with Hydrogen
        Mass Repartitioning if ATOMIC_NUMBER is not
        present in the topology file
--------------------------------------------------

Apparently this error is caused by the qmmm_module.F90 module,
presumably due to the shape or mass with which the Zinc atom is defined
in the Pang YP model.

I would appreciate any suggestions to circumvent this error.
Greetings,
Hector.

-- 
--------------------------------------
  Dr. Hector A. Baldoni
  Profesor Titular (FQByF-UNSL)
  Investigador Adjunto (IMASL-CONICET)
  Area de Quimica General e Inorganica
  Universidad Nacional de San Luis
  Chacabuco 917 (D5700BWS)
  San Luis - Argentina
  hbaldoni at unsl dot edu dot ar
  Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
I do not define time, space, place, and motion, as being well known to 
all.
-- Newton (1642-1726), Principia
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Received on Tue Jul 18 2023 - 15:00:02 PDT
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