Hi
I tried xmin minimizer by setting ntmin=3. It turns out pmemd does not
support ntmin=3. So i tried sander.MPI with ntmin=3 and 1. But somehow it
throws error for the same input which pmemd runs fine.
I think there is some format difference in input of sander and pmemd in
case of input file which i am unable to point out. I have tried several
different variations none yielded a positive result.
Can you help me out in finding this difference.
*The output says:* LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
defa
----- READING GROUP 1; TITLE:
simulated annealing protocol, 20 ps
rfree: Error decoding variable 1 3 from:
&cntrl
this indicates that your input contains
incorrect information
field 1 was supposed to
have a (1=character, 2=integer, 3=decimal) value
*in file says:*simulated annealing protocol, 20 ps
&cntrl
imin=1, ntx=1, irest=0, ntpr=50, ntf=1, ntb=1, ntmin=3,
cut=9.0, nsnb=10, ntr=1, maxcyc=5000, ncyc=2000, nmropt=1,
/
&wt type='REST', istep1=0,istep2=1500,value1=1.0, value2=1.0, /
&wt type='REST', istep1=1501,istep2=5000,value1=1.0, value2=1.0, /
&wt type='END' /
LISTOUT=POUT
DISANG=restraints
&end
* the restraints file reads as (as it has non bonded ion and water
prepared through MCPB.py):*
# Harmonic restraints for the restrained nonbonded model of comp
&rst iat=453,6526, r1=0., r2=2.0741, r3=2.0741, r4=100., rk2=32.4000,
rk3=32.4000,/
&rst iat=6526,6534, r1=0., r2=2.0336, r3=2.0336, r4=100., rk2=44.2000,
rk3=44.2000,/
&rst iat=6526,6533, r1=0., r2=1.9882, r3=1.9882, r4=100., rk2=69.0000,
rk3=69.0000,/
&rst iat=6526,6538, r1=0., r2=2.1393, r3=2.1393, r4=100., rk2=30.6000,
rk3=30.6000,/
&rst iat=6526,6570, r1=0., r2=2.1012, r3=2.1012, r4=100., rk2=46.6000,
rk3=46.6000,/
&rst iat=6526,6573, r1=0., r2=2.1097, r3=2.1097, r4=100., rk2=43.8000,
rk3=43.8000,/
&rst iat=6529,6600, r1=0., r2=1.7272, r3=1.7272, r4=100., rk2=43.8000,
rk3=43.8000,/
&rst iat=392,6599, r1=0., r2=1.6389, r3=1.6389, r4=100., rk2=43.8000,
rk3=43.8000,/
On Tue, May 1, 2018 at 5:31 AM, Goetz, Andreas <agoetz.sdsc.edu> wrote:
> 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 Tue May 01 2018 - 06:30:02 PDT
