Hi Kankana,
Can you leave a black space below the "&" character till "/" for each
section and try again? The input looks something like this:
&cntrl
imin=0, irest=1, ntx=5,
...............................,
ifqnt=1,
/
&qmmm
qmmask = ':1,308,4,62, .........',
....................................,
qm_ewald = 0,
/
&quick
method = 'B3LYP',
basis = 'def2-svp',
/
*Best,*
*Satyajit Khatua*
On Sat, Jan 4, 2025 at 10:11 PM Kankana Bhattacharjee via AMBER <
amber.ambermd.org> wrote:
> Dear sir,
>
> Thanks a lot for your suggestions.
> I have modified the qmmm.in file based on your instructions. But, still
> getting the same error. I am attaching my qmmm.in file herewith. Kindly
> give me some suggestions.
>
> Thanks and Regards
> Kankana Bhattacharjee
>
> On Sat, Jan 4, 2025 at 3:17 AM Goetz, Andreas <awgoetz.ucsd.edu> wrote:
>
> > 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*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
> >
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!Mih3wA!FucBHX3NNmLJfwiVRb7onOMYqiGj7BiHh2F0FKi9nTtv62b8jKbgjPzpHRu9QyXl0PfoP8A6tgqs5g$
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 04 2025 - 20:00:03 PST
