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*
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- application/octet-stream attachment: qmmm.in
Received on Sat Jan 04 2025 - 19:30:02 PST
