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
