The error is with the &cntrl namelist. It looks like you may have a tab or other invisible character in front of &cntrl. Only space characters will work. Remove any empty space in front of &cntrl and try again.
You will need to set ifqnt = 1 in the &cntrl namelist to enable QM/MM.
I also recommend setting ntpr = 1. DFT based QM/MM is much slower than MM. Hence it does not hurt to print info every step (although QUICK output will be written to quick.out every time step). You may also want to set ntwx =1, at least initially, to visualize the trajectory in case something goes wrong.
All the best,
Andy
—
Dr. Andreas W. Goetz
Associate Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
On Jan 3, 2025, at 10:52 AM, Kankana Bhattacharjee via AMBER <amber.ambermd.org> wrote:
Dear AMBER users,
I have tried top generate a qmmm input file based on API. This is my input
file:
&cntrl
imin=0,irest=1,ntx=5,
nstlim=20000,dt=0.001,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=50, ntwx=50,
ntt=3, gamma_ln=2.0,
temp0=300.0, ig=-1,
/
&qmmm
qmmask =
':1,308,4,62,15,361,68,95,321,71,38,37,324,436,445,133,155,142,177,212,75,64,255,7',
qm_theory = 'quick',
qmmm_int = 1,
qm_ewald = 0,
/
&quick
method = 'B3LYP',
basis = 'def2-svp',
/
I have used this command line: sander.quick.cuda -O -i qmmm.in -o qmmm.out
-p lig-solv.prmtop -c equil.rst -r qmmm.rst -x qmmm.mdcrd
But, it seems qmmm could not run and qmmm.out is having this problem:
*Could not find cntrl namelist*
*It would be really great, if you kindly give some suggestions. *
*Thanks & Regards*
*Kankana Bhattacharjee*
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Received on Fri Jan 03 2025 - 14:00:02 PST
