On Fri, 2014-02-21 at 06:34 -0700, Daniel Roe wrote:
> Hi,
>
> On Friday, February 21, 2014, Saeed Nasiri <s.t.nasiri.gmail.com> wrote:
> >
> > Thanks for your useful reply. I used the parmed.py (I do minimization
> > again with new files ionicbox2.* successfully), but the output file maybe
> > has some defect, for example the .incprd file does not include the box
> > information,
>
>
> Just to be clear, is it ionicbox2.inpcrd that does not have box info? Does
> this mean that when you said you completed minimization successfully, you
> performed it using implicit solvent? Or are you implying that after
> minimization the box information was somehow removed? I'm not sure why your
> minimization would be successful but your MD not.
>
> or when the box information was add to end of the file an
> > error that is related to periodicity was appeared. Also I change the ifbox
> > to one (the 28th number in %FLAG POINTERS %FORMAT(10I8) in prmtop file ),
> > but again the fallowing error was appeared?
>
>
> You should avoid edtiting the topology file by hand; it is way too easy for
> things to go wrong.
>
> Out of curiosity, have you tried the 'fixatomorder' command in cpptraj?
I suggest trying 'fixatomorder' in cpptraj. I suspect what happened is
that your system does not have any water in it (with residue names HOH
or WAT) -- is this true? When ParmEd detects no solvent is present, it
automatically deletes all box information because that usually indicates
you are trying to set up an implicit solvent system. You can use the
"defineSolvent" command in ParmEd to supply a list of residues that
should be considered 'solvent'. If you supply your solvent residues to
this command then ParmEd will keep the box information.
cpptraj, on the other hand, will only get rid of box information if you
explicitly ask it to. This difference in behavior stems from
differences in the scope of each program. ParmEd is aimed at preparing
modifications for new simulations whereas cpptraj is aimed as much at
postprocessing trajectories as preparing systems. It is often useful to
have box information in stripped topologies/trajectories if you need to
re-image later on.
Hopefully this helps explain the behavior you're seeing. Don't forget
to create a new inpcrd/restart file with your 'fixed' prmtop since the
atom ordering will change and the two files need to be compatible.
Good luck,
Jason
>
> -Dan
>
>
> > Is it possible to fix the file completely?
> >
> > Your Sincerely
> > S. Nasiri
> >
> > ======================parmed.py============================
> > parmed.py -p ionicbox.prmtop
> >
> > ./ | | \.
> > .:( |i __ j| ):`.
> > .' `._ |`::::'| _.' `.
> > .' "---.j `::' f.---" `.
> > _____/ ___ ____ __ __ ____ ___
> > | \ | | | `__'| \ / || | | \
> > | .-. | .' `| | .-. |-/| \/ || ___| | . \
> > | |_| | | i | | |_| /"":| || | | | \ \
> > | / | .^. | | /::::| || |__. | | \ \
> > | ----' | | | | | \ :: | || __| | | | )
> > | | .' ''' `.| |\ \ | i i j| | . | / /
> > | | | _ || | \ \ | |\/| || |__. | |. / .
> > [| | | | | || | \ \ | | | || | | / ].
> > ] `--' :--' `--::--' \_|`--' ::--"|____|-"-- / :[
> > | __ ::-'''`.:' "--. .----::.----:: ,.---._ :|
> > [ .-"" "`' \ / " `' `-. :].
> > ]:.' \/ `.:[
> > |/ \|
> >
> > ParmEd: a Parameter file Editor
> >
> >
> > Loaded Amber topology file ionicbox.prmtop
> >
> > Reading input from STDIN...
> > > loadRestrt ionicbox.inpcrd
> > Loading restart file ionicbox.inpcrd
> > > checkValidity
> > Determining validity of prmtop
> > 1 total warnings
> >
> > FixableParmWarning: sum(ATOMS_PER_MOLECULE) != NATOM. Use "setMolecules" to
> > fix
> > this
> >
> > > setMolecules ATOMS_PER_MOLECULE=true
> > /home/nasiri/amber12/bin/ParmedTools/ParmedActions.py:879: UserWarning:
> > Value of solute_ions is unrecognized [ATOMS_PER_MOLECULE=true]! Assuming
> > True
> > solute_ions + "Assuming True")
> > Setting MOLECULE properties of the prmtop (SOLVENT_POINTERS and
> > ATOMS_PER_MOLECULE)
> > > outparm ionicbox2.prmtop ionicbox2.inpcrd
> > Outputting Amber topology file ionicbox2.prmtop and restart
> > ionicbox2.inpcrd
> > > quit
> > Done!
> > =====================pmemd.MPI============================
> >
> > mpirun -np 4 pmemd.MPI -O -i mdin.in -o md1.out -p ionicbox2.prmtop -c
> > min.x -r md1.x -x md1.nc -e md1.dat
> > --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> > --------------------------------------------------------------------------
> > forrtl: error (78): process killed (SIGTERM)
> > Image PC Routine Line
> > Source
> > libmpi.so.1 00007F7B5530BDB2 Unknown Unknown Unknown
> > libmpi.so.1 00007F7B5523E9A2 Unknown Unknown Unknown
> > mca_coll_tuned.so 00007F7B4DF670B0 Unknown Unknown Unknown
> > mca_coll_tuned.so 00007F7B4DF66CCD Unknown Unknown Unknown
> > mca_coll_tuned.so 00007F7B4DF5DD9D Unknown Unknown Unknown
> > mca_coll_sync.so 00007F7B4E17C64D Unknown Unknown Unknown
> > libmpi.so.1 00007F7B5524D14D Unknown Unknown Unknown
> > libmpi_f77.so.1 00007F7B555FC106 Unknown Unknown Unknown
> > pmemd.MPI 0000000000526634 Unknown Unknown Unknown
> > pmemd.MPI 000000000041E48C Unknown Unknown Unknown
> > libc.so.6 00007F7B52AC276D Unknown Unknown Unknown
> > pmemd.MPI 000000000041E389 Unknown Unknown Unknown
> > forrtl: error (78): process killed (SIGTERM)
> > Image PC Routine Line
> > Source
> > mca_btl_sm.so 00007F189A6D53C9 Unknown Unknown Unknown
> > libmpi.so.1 00007F18A0BB5E39 Unknown Unknown Unknown
> > libmpi.so.1 00007F18A0AE89A2 Unknown Unknown Unknown
> > mca_coll_tuned.so 00007F18998112A4 Unknown Unknown Unknown
> > mca_coll_tuned.so 00007F1899810CCD Unknown Unknown Unknown
> > mca_coll_tuned.so 00007F1899807D9D Unknown Unknown Unknown
> > mca_coll_sync.so 00007F1899A2664D Unknown Unknown Unknown
> > libmpi.so.1 00007F18A0AF714D Unknown Unknown Unknown
> > libmpi_f77.so.1 00007F18A0EA6106 Unknown Unknown Unknown
> > pmemd.MPI 0000000000526634 Unknown Unknown Unknown
> > pmemd.MPI 000000000041E48C Unknown Unknown Unknown
> > libc.so.6 00007F189E36C76D Unknown Unknown Unknown
> > pmemd.MPI 000000000041E389 Unknown Unknown Unknown
> > forrtl: error (78): process killed (SIGTERM)
> > Image PC Routine Line
> > Source
> > libmpi.so.1 00007FBFEA69DDAB Unknown Unknown Unknown
> > libmpi.so.1 00007FBFEA5D09A2 Unknown Unknown Unknown
> > mca_coll_tuned.so 00007FBFE32F92A4 Unknown Unknown Unknown
> > mca_coll_tuned.so 00007FBFE32F8CCD Unknown Unknown Unknown
> > mca_coll_tuned.so 00007FBFE32EFD9D Unknown Unknown Unknown
> > mca_coll_sync.so 00007FBFE350E64D Unknown Unknown Unknown
> > libmpi.so.1 00007FBFEA5DF14D Unknown Unknown Unknown
> > libmpi_f77.so.1 00007FBFEA98E106 Unknown Unknown Unknown
> > pmemd.MPI 0000000000526634 Unknown Unknown Unknown
> > pmemd.MPI 000000000041E48C Unknown Unknown Unknown
> > libc.so.6 00007FBFE7E5476D Unknown Unknown Unknown
> > pmemd.MPI 000000000041E389 Unknown Unknown Unknown
> > --------------------------------------------------------------------------
> > mpirun has exited due to process rank 0 with PID 4075 on
> > node nasiri-desktop exiting improperly. There are two reasons this could
> > occur:
> >
> > 1. this process did not call "init" before exiting, but others in
> > the job did. This can cause a job to hang indefinitely while it waits
> > for all processes to call "init". By rule, if one process calls "init",
> > then ALL processes must call "init" prior to termination.
> >
> > 2. this process called "init", but exited without calling "finalize".
> > By rule, all processes that call "init" MUST call "finalize" prior to
> > exiting or it will be considered an "abnormal termination"
> >
> > This may have caused other processes in the application to be
> > terminated by signals sent by mpirun (as reported here).
> >
> > =====================md1.out===========================
> > ionicbox2.inpcrd
> >
> > -------------------------------------------------------
> > Amber 12 SANDER 2012
> > -------------------------------------------------------
> >
> > | PMEMD implementation of SANDER, Release 12
> >
> > | Run on 02/21/2014 at 12:16:22
> >
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: mdin.in
> >
> > | MDOUT:
> > md1.out
> > | INPCRD:
> > min.x
> > | PARM:
> > ionicbox2.prmtop
> > | RESTRT:
> > md1.x
> > | REFC:
> > refc
> > | MDVEL:
> > mdvel
> > | MDEN:
> > md1.dat
> > | MDCRD: md1.nc
> >
> > | MDINFO:
> > mdinfo
> > |LOGFILE:
> > logfile
> >
> >
> > Here is the input file:
> >
> > &cntrl
> >
> > imin=0, ntpr=10000,
> > ntwx=10000,
> > ntx=1,
> > irest=0,
> > tempi=298., temp0=298.,
> > ntt=3,
> > gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1,
> > nstlim=2000000,
> > ntwr=1000, dt=.001, ig=-1,
> > cut=12,
> > &end
> >
> >
> >
> >
> >
> > Note: ig = -1. Setting random seed based on wallclock time in microseconds
> > and disabling the synchronization of random numbers between tasks
> > to improve performance.
> >
> >
> > | Conditional Compilation Defines Used:
> > | DIRFRC_COMTRANS
> > | DIRFRC_EFS
> > | DIRFRC_NOVEC
> > | MPI
> > | PUBFFT
> > | FFTLOADBAL_2PROC
> > | BINTRAJ
> >
> > | Largest sphere to fit in unit cell has radius = 14.992
> >
> > | New format PARM file being parsed.
> > | Version = 1.000 Date = 02/21/14 Time = 12:14:56
> >
> > | Note: 1-4 EEL scale factors are being read from the topology file.
> >
> > | Note: 1-4 VDW scale factors are being read from the topology file.
> > | Duplicated 0 dihedrals
> >
> > | Duplicated 0 dihedrals
> >
> >
> > --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> >
> > --------------------------------------------------------------------------------
> >
> > getting new box info from bottom of inpcrd
> >
> > NATOM = 1744 NTYPES = 10 NBONH = 1144 MBONA = 336
> > NTHETH = 2056 MTHETA = 96 NPHIH = 1160 MPHIA = 136
> > NHPARM = 0 NPARM = 0 NNB = 5136 NRES = 264
> > NBONA = 336 NTHETA = 96 NPHIA = 136 NUMBND = 12
> > NUMANG = 21 NPTRA = 11 NATYP = 11 NPHB = 0
> > IFBOX = 0 NMXRS = 26 IFCAP = 0 NEXTRA = 0
> > NCOPY = 0
> >
> > | Coordinate Index Table dimensions: 4 4 4
> > | Direct force subcell size = 7.4997 7.5000 7.4958
> >
> >
> > --------------------------------------------------------------------------------
> > 2. CONTROL DATA FOR THE RUN
> >
> > --------------------------------------------------------------------------------
> >
> > default_name
> >
> >
> > General flags:
> > imin = 0, nmropt = 0
> >
> > Nature and format of input:
> > ntx = 1, irest = 0, ntrx = 1
> >
> > Nature and format of output:
> > ntxo = 1, ntpr = 10000, ntrx = 1, ntwr =
> > 1000
> > iwrap = 0, ntwx = 10000, ntwv = 0, ntwe
> > = 0
> > ioutfm = 1, ntwprt = 0, idecomp = 0,
> > rbornstat= 0
> >
> > Potential function:
> > ntf = 1, ntb = 2, igb = 0, nsnb
> > = 25
> > ipol = 0, gbsa = 0, iesp = 0
> > dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
> >
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 0
> >
> > Molecular dynamics:
> > nstlim = 2000000, nscm = 1000, nrespa = 1
> > t = 0.00000, dt = 0.00100, vlimit = 20.00000
> >
> > Langevin dynamics temperature regulation:
> > ig = 861614
> > temp0 = 298.00000, tempi = 298.00000, gamma_ln= 5.00000
> >
> > Pressure regulation:
> > ntp = 1
> > pres0 = 1.00000, comp = 44.60000, taup = 1.00000
> >
> > | Intermolecular bonds treatment:
> > | no_intermolecular_bonds = 1
> >
> > | Energy averages sample interval:
> > | ene_avg_sampling = 10000
> >
> > Ewald parameters:
> > verbose = 0, ew_type = 0, nbflag = 1, use_pme
> > = 1
> > vdwmeth = 1, eedmeth = 1, netfrc = 1
> > Box X = 29.999 Box Y = 30.000 Box Z = 29.983
> > Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> > NFFT1 = 30 NFFT2 = 30 NFFT3 = 30
> > Cutoff= 12.000 Tol =0.100E-04
> > Ewald Coefficient = 0.22664
> > Interpolation order = 4
> >
> > | PMEMD ewald parallel performance parameters:
> > | block_fft = 0
> > | fft_blk_y_divisor = 2
> > | excl_recip = 0
> > | excl_master = 0
> > | atm_redist_freq = 320
> > | ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported!
> > Input errors occurred. Terminating execution.
> >
> > =====================change IFBOX==========================
> > ionicbox2.prmtop
> >
> > ********************initial ******************************
> >
> > %VERSION VERSION_STAMP = V0001.000 DATE = 02/21/14 12:14:56
> > %FLAG TITLE
> > %FORMAT(20a4)
> > default_name
> > %F
>
>
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 21 2014 - 06:30:02 PST
