Dear Amber community,
I am performing QM/MM simulations with Amber 20 and Orca 5.0. I would like to report a problem when including water molecules in the QM partition using Sander (Amber 20).
The water molecules inside the QM partition appear with wrong H-O-H angles (~70 º) and short O-H distances (~0.7-0.8 A) already in the first frame of the QM/MM simulation. The water molecules minimized with MM had correct parameters prior to the QM/MM job. This strange water molecule distortions are not solved during the QM/MM minimization.
My guess is that there is a problem in the subroutine that extracts the coordinates from the whole system and prepares the .xyz files for the QM program. Is this a known problem? Am I including any incorrect keyword? Find below the minimization input I use.
Many thanks for your help.
Best regards,
Antonio Francés
Physical Chemistry Department
University of Valencia (Spain)
INPUT:
production
&cntrl
! TYPE OF JOB (MINIMIZATION)
imin=1,
! GENERAL KEYWORDS
iwrap=1,
irest=0,
ntx=1,
igb=0,
cut=9.0,
ifqnt=1,
nmropt = 1,
! MINIMIZATION KEYWORDS (ONLY APPLY IF IMIN = 1)
maxcyc=50,
ntmin=1,
ncyc=25,
ntpr=5,
! PRODUCTION KEYWORDS
dt=0.001,
ntpr=1,
ntwx=1,
ntwv=-1,
ntwr=5
ntt=3,gamma_ln=1,
temp0=0.0,
ntp=0,
ntb=1,
ntf=2,ntc=2,
/
! QM/MM SECTION
&qmmm
qmmask = '.1-18,41-62,85-116,5174-5176,1589-1591',
qmcharge = 2,
spin = 3,
qm_ewald = 0,
qmcut = 9.0,
qmshake=1,
qm_theory = 'EXTERN',
/
&orc
use_template=1,
/
!RESTRAINTS SECTION
&wt type='DUMPFREQ', istep1=5, /
&wt
type='END',
&end
DISANG=disang.2.0
DUMPAVE=Pt-Cl_vs_t_min.2.0
DISANG FILE:
Harmonic restraints for 2.0 angstrom
&rst
iat=5174,114,
r1=-3,r2=2.0,r3=2.0,r4=7,
rk2=3000.0, rk3=3000.0,
/
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Received on Mon Jan 17 2022 - 08:00:02 PST
