Your problem is probably not related to QM/MM. Maybe try optimizing with MM before attempting a QM/MM optimization. In this way your MM environment is already relaxed and in a subsequent QM/MM optimization you should see mostly changes in the QM region and around the QM/MM boundary. Also note that the default optimizer in Amber is not very efficient and requires many steps to converge. You can try the xmin optimizer (set ntmin = 3), which provides algorithms that are quadratically convergent - these converge much faster, but are still expensive due to repeated energy/force evaluations during the line search.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>
Web: www.awgoetz.de<http://www.awgoetz.de>
On Apr 30, 2018, at 1:16 AM, Abhilash J <md.scfbio.gmail.com<mailto:md.scfbio.gmail.com>> wrote:
Hi everyone,
I am trying to perform QM/MM MD on a ligand and some residues in the
active site of a protein.
I did a 10 ns production of the complex using classical MD then tried
minimization using QM/MM in AMBER with Gaussian.
I am getting linear minimization error on one of the water molecules
in the bulk water around the protein.
I tried different initial structures but the problem persists. (Every
time error was with a water residue in the bulk, only the residue number
changed)
I do not understand how the structure is running ok with GPU but not
getting into LINMIN error in CPU(s).
I also removed all but 1 water molecule from the list of atoms for QM
problem still persisted.
I tried changing number of CPUs in both gaussian and sander (sander
and sander.MPI).
I am using AMBER 18 with Gaussian 09
*My input file is like this:*
==========================================
Initial min of our structure QMMM
&cntrl
imin=1, maxcyc=2000, ncyc=1000,
cut=8.0, ntb=1, ntc=2, ntf=2,
ifqnt=1
/
&qmmm
qmmask=':429'
qmcharge=0,
qmshake=0,
qm_ewald=0, qm_pme=1,
qm_theory='EXTERN',
spin=1,
/
&gau
mem = '25GB',
method = 'B3LYP',
basis = '6-31G(d)',
num_threads = 12,
use_template = 0,
/
==========================================
*Error on CPU using sander is like this:*
===========================================
NSTEP ENERGY RMS GMAX NAME NUMBER
950 -1.7584E+05 1.4842E+01 5.0996E+01 O 14380
BOND = 296.7775 ANGLE = 1192.8399 DIHED =
4758.5891
VDWAALS = 8241.4047 EEL = -162581.2527 HBOND =
0.0000
1-4 VDW = 1340.3387 1-4 EEL = 18890.8303 RESTRAINT =
0.0000
EXTERNESCF = -47974.7606
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -1.7584E+05 1.4842E+01 5.0996E+01 O 14380
BOND = 296.7775 ANGLE = 1192.8392 DIHED =
4758.5888
VDWAALS = 8241.4014 EEL = -162581.2432 HBOND =
0.0000
1-4 VDW = 1340.3386 1-4 EEL = 18890.8303 RESTRAINT =
0.0000
EXTERNESCF = -47974.7606
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
1050 -1.7584E+05 1.4842E+01 5.0996E+01 O 14380
BOND = 296.7774 ANGLE = 1192.8391 DIHED =
4758.5888
VDWAALS = 8241.4006 EEL = -162581.2406 HBOND =
0.0000
1-4 VDW = 1340.3386 1-4 EEL = 18890.8303 RESTRAINT =
0.0000
EXTERNESCF = -47974.7606
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
1100 -1.7584E+05 1.4842E+01 5.0996E+01 O 14380
BOND = 296.7774 ANGLE = 1192.8388 DIHED =
4758.5887
VDWAALS = 8241.3995 EEL = -162581.2369 HBOND =
0.0000
1-4 VDW = 1340.3385 1-4 EEL = 18890.8302 RESTRAINT =
0.0000
EXTERNESCF = -47974.7606
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
===========================================
*pmemd.cuda output is like this:*
===========================================
NSTEP = 3350000 TIME(PS) = 12100.000 TEMP(K) = 298.79 PRESS =
348.3
Etot = -95866.3616 EKtot = 24492.4648 EPtot =
-120358.8265
BOND = 1220.3755 ANGLE = 3352.1816 DIHED =
5147.2619
1-4 NB = 1494.6215 1-4 EEL = 18923.0385 VDWAALS =
11982.1028
EELEC = -162485.2678 EHBOND = 0.0000 RESTRAINT =
6.8594
EAMBER (non-restraint) = -120365.6859
EKCMT = 9700.3856 VIRIAL = 6770.2280 VOLUME =
389629.2225
Density =
1.0463
------------------------------------------------------------------------------
NMR restraints: Bond = 6.859 Angle = 0.000 Torsion = 0.000
===============================================================================
===========================================
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Received on Mon Apr 30 2018 - 17:30:03 PDT
