[gmx-users] QM/MM with gromacs 2016

[Sylwia Kacprzak]

Dear all,

I am new to qm/mm calculations. Before trying my own calculations, I 
have tried to
run the tutorial on thymine dimer repair 
(http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/tutorial.html).
I have downloaded all the files from the tutorial (mdout.mdp qmmm1.gro  
qmmm1.mdp  qmmm.ndx  qmmm.top).

However after running the command
gmx grompp -f qmmm1.mdp -p qmmm.top -n qmmm.ndx -c qmmm1.gro

I have a number of errors (please look below).

Can anyone help me further with this problems?

Best greetings
Sylwia



NOTE 1 [file qmmm1.mdp, line 89]:
   qmmm1.mdp did not specify a value for the .mdp option "cutoff-scheme".
   Probably it was first intended for use with GROMACS before 4.6. In 4.6,
   the Verlet scheme was introduced, but the group scheme was still the
   default. The default is now the Verlet scheme, so you will observe
   different behaviour.

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'domain-decomposition'
Ignoring obsolete mdp entry 'nstcheckpoint'
Ignoring obsolete mdp entry 'optimize_fft'
Replacing old mdp entry 'unconstrained_start' by 'continuation'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#

NOTE 2 [file qmmm1.mdp]:
   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
   that with the Verlet scheme, nstlist has no effect on the accuracy of
   your simulation.


NOTE 3 [file qmmm1.mdp]:
   Setting nstcalcenergy (100) equal to nstenergy (10)


NOTE 4 [file qmmm1.mdp]:
   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
   nstcomm to nstcalcenergy


NOTE 5 [file qmmm1.mdp]:
   The Berendsen thermostat does not generate the correct kinetic energy
   distribution. You might want to consider using the V-rescale thermostat.


ERROR 1 [file qmmm1.mdp]:
   QMMM is currently only supported with cutoff-scheme=group

Setting the LD random seed to -1378559983
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations

-------------------------------------------------------
Program:     gmx grompp, version 2016
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1343)

Fatal error:
Atomtype amber99_25 not found

For more information and tips for troubleshooting, please check the GROMACS