Re:Re: Wrong number of basis-sets stored!

From: 辛志宏 (
Date: Wed Sep 02 2020 - 09:48:38 CDT

Dear Atanu,
Think you very much for your kindly suggestion.
I checked qmBaseDir using an namd QM/MM example (namd-QM-MM-Example) when I changed " QMSimsPerNode 10 " as " QMSimsPerNode 1', It works fine in the Dir "/dev/shm/NAMD_Example1",

However, a new errors occured again for my enzyme simulation,

[xzhfood_at_bogon YZZ-QM-MM]$ namd2 YZZ-config.ORCA-1.namd | tee YZZ-config.ORCA-1.namd.log
Charm++> No provisioning arguments specified. Running with a single PE.
         Use +auto-provision to fully subscribe resources or +p1 to silence this message.
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads (PEs)
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.10.0-rc2-9-g717093c-namd-charm-6.10.0-build-2019-Oct-31-14158
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 hosts (2 sockets x 28 cores x 2 PUs = 112-way SMP)
Charm++> cpu topology info is gathered in 0.008 seconds.
Info: NAMD Git-2019-12-13 for Linux-x86_64-multicore
Info: Please visit
Info: for updates, documentation, and support information.
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: Based on Charm++/Converse 61000 for multicore-linux-x86_64-iccstatic
Info: Built Fri Dec 13 02:06:04 CST 2019 by jim on
Info: 1 NAMD Git-2019-12-13 Linux-x86_64-multicore 1 bogon xzhfood
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0148728 s
CkLoopLib is used in SMP with simple dynamic scheduling (converse-level notification)
Info: 64.1562 MB of memory in use based on /proc/self/stat
Info: Configuration file is YZZ-config.ORCA-1.namd
Info: Working in the current directory /home/xzhfood/mdsim/YZZ-namd/YZZ-QM-MM
------------- Processor 0 Exiting: Called CmiAbort ------------

TCL: Suspending until startup complete.
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: Continuing

There is no .TmpOut file in my workdir, I don't know why the same parameters for the namd example works, and don't works for my enzyme , why switch to the current Dir " Working in the current directory /home/xzhfood/mdsim/YZZ-namd/YZZ-QM-MM"not "/dev/shm/NAMD_Example1", I also build a new Dir as "/dev/shm/YZZ-namd", and chmod +x "/dev/shm/YZZ-namd" make sure it is writable, but the error is the same.
Thank you for your help again.

Zhihong Xin

发件人:"Acharya, Atanu" <>
发送日期:2020-09-02 13:10:54
收件人:"" <>,"辛志宏" <>
主题:Re: namd-l: Wrong number of basis-sets stored!
Dear Zhihong,

Look in your qmBaseDir, where ORCA is writing intermediate files.
In your case, It is /dev/shm/NAMD_Example1

You should see a .TmpOut file which is written by ORCA for the current QM/MM step.
Since it is an ORCA specific error the TmpOut file may provide more details about the error.

One thing I did notice in your conf file that may raise some problem.
You specified to have 10 QM calculations while passing charge/multiplication information for only one qm region.
qmMult "1 2"
qmCharge "1 -1"

I assumed you have 10 qm regions since you requested:

# Number of simultaneous QM simulations per node
QMSimsPerNode 10


On Sep 1, 2020, at 10:10 PM, 辛志宏 <> wrote:

Deal Namd,

I came across a issue when I run a QM/MM simulation,

TCL: Minimizing for 100 steps
Info: List of ranks running QM simulations: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9.
[file orca_tools/Tool-GTO-Bases/basissets.cpp, line 706]: Wrong number of basis-sets stored!

FATAL ERROR: Error reading QM forces file.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error reading QM forces file.

I do not find the solution in the mailing list and ask for help, any suggestion will be much appreciate.

My Namd config file as follows:

# This is a namd configuration file

## Single QM region with MM water box
structure ./ionized.psf
coordinates ./YZZ-namd-equil-last-1.pdb

# Continuing a job from the restart files
if {1} {
set inputname ../YZZ_equil_MM
binCoordinates $inputname.coor
#binVelocities $inputname.vel ;# remove the "temperature" entry if you use this!
extendedSystem $inputname.xsc

cellBasisVector1 64.945 0 0
cellBasisVector2 0 65.353 0
cellBasisVector3 0 0 67.919
cellOrigin 55.318 57.874 55.561

seed 7910881

# Output Parameters

binaryoutput no
outputname ./YZZ-QM-min-out
outputenergies 1
outputtiming 1
outputpressure 1
binaryrestart yes
dcdfile ./YZZ-QM-min-out.dcd
dcdfreq 1
XSTFreq 1
restartfreq 100
restartname ./YZZ-QM-min-out.restart

# mobile atom selection:

constraints on
consexp 2
consref ./YZZ-restraint.pdb
conskfile ./YZZ-restraint.pdb
conskcol B
constraintScaling 5.0

# PME Parameters

PME on
PMEGridspacing 1

set temperature 300

temperature $temperature

# Thermostat Parameters

langevin on
langevintemp $temperature
langevinHydrogen on
langevindamping 50

# Barostat Parameters

usegrouppressure yes
useflexiblecell no
useConstantArea no
langevinpiston on
langevinpistontarget 1.01325
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp $temperature
surfacetensiontarget 0.0
strainrate 0. 0. 0.

wrapAll on
wrapWater on

# Integrator Parameters

timestep 0.5
firstTimestep 0
fullElectFrequency 1
nonbondedfreq 1

# Force Field Parameters

paratypecharmm on
parameters ../CHARMpars/toppar_all36_carb_glycopeptide.str
parameters ../CHARMpars/toppar_water_ions_namd.str
parameters ../CHARMpars/toppar_all36_na_nad_ppi_gdp_gtp.str
parameters ../CHARMpars/par_all36_carb.prm
parameters ../CHARMpars/par_all36_cgenff.prm
parameters ../CHARMpars/par_all36_lipid.prm
parameters ../CHARMpars/par_all36_na.prm
parameters ../CHARMpars/par_all36_prot.prm
parameters ../common/DMP_ABD769.prm

#printExclusions on
exclude scaled1-4
1-4scaling 1.0
rigidbonds none
cutoff 12.0
pairlistdist 14.0
switching on
switchdist 10.0

stepspercycle 1

# Truns ON or OFF the QM calculations
qmForces on

qmParamPDB "./YZZ-namd-QM-0.pdb"

qmColumn "beta"

qmBondColumn "occ"

#Link Atoms

#qmBondDist on


# Number of simultaneous QM simulations per node
QMSimsPerNode 10

QMElecEmbed on

QMSwitching on

QMSwitchingType shift

QMPointChargeScheme none

QMBondScheme "cs"

qmBaseDir "/dev/shm/NAMD_Example1"

qmConfigLine "! B3LYP 6-31G Grid4 PAL4 EnGrad TightSCF"

qmConfigLine "%%output PrintLevel Mini Print\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end"

# construction of ORCA's input file.
qmMult "1 2"

qmCharge "1 -1"

qmSoftware "orca"

qmExecPath "/home/xzhfood/software/orca_4_1_2_linux_x86-64_openmpi313/orca"
QMOutStride 1
QMPositionOutStride 1

# Number of steps in the QM/MM simulation.
minimize 100
run 2000

Zhihong Xin

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