Hi,
On Thu, Mar 20, 2014 at 9:31 AM, Saeed Nasiri <s.t.nasiri.gmail.com> wrote:
> because I faced with another error "ERROR: the combination ntb != 0, ntp
> != 0, ifbox == 0 is not supported! Input errors occurred. Terminating
> execution."
>
This error is sensible - if there is no box information in your topology
you cannot run a periodic simulation. Either your original topology doesn't
have box info, or somewhere along the way you may have lost your box info.
You could try using the following cpptraj input to set your solvent info:
parm input.parm7
solvent :MTO
parmwrite out solvent.input.parm7
This will only work if the original topology has the correct box
information set. You can check this by loading your topology in cpptraj and
typing 'parminfo' (check the 'Box:' line), e.g.:
[]$ cpptraj full.topo
CPPTRAJ: Trajectory Analysis. V13.24
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
AmberParm Title: []
Radius Set: modified Bondi radii (mbondi)
Warning: [full.topo] ATOMIC_NUMBER not present in topology.
> parminfo
Topology full.topo contains 7622 atoms.
2504 residues.
7628 bonds.
2501 molecules.
Box: Trunc. Oct.
2497 solvent molecules.
Final solute residue is 7
-Dan
> Also I set methanol as solvent (MTO residues) as you said.
>
> Your Sincerely
> Nasiri
>
>
>
>
>
> ====================================parmed.py===========================================
>
>
> parm ionicbox.prmtop
> defineSolvent:MTO
> setMolecules solute_ions True
> parmout ionicbox2.prmtop
>
>
>
> parmed.py -i parm.in
>
> Y O U H A V E B E E N
> _
> ==(W{==========- /===-
> || (.--.)
> /===-_---~~~~~~~~~------____
> | \_,|**|,__ |===-~___
> _,-' `
> -==\\ `\ ' `--' ), `//~\\ ~~~~`---.___.-~~
> ______-==| /`\_. .__/\ \ | | \\ _-~`
> __--~~~ ,-/-==\\ ( | . |~~~~| | | `\ ,'
> _-~ /' | \\ )__/==0==-\<>/ / / \ /
> .' / | \\ /~\___/~~\/ /' / \ /'
> / ____ / | \`\.__/-~~ \ |_/' / \/'
> /-'~ ~~~~~---__ | ~-/~ ( ) /' _--~`
> \_| / _) | ; ), __--~~
> '~~--_/ _-~/- |/ \ '-~ \
> {\__--_/} / \\_>-|)<__\ \
> /' (_/ _-~ | |__>--<__| |
> | _/) )-~ | |__>--<__| |
> / /~ ,_/ / /__>---<__/ |
> o-o _// /-~_>---<__-~ /
> (^(~ /~_>---<__- _-~
> ,/| /__>--<__/ _-~
> ,//('( |__>--<__| / .----_
> ( ( ')) |__>--<__| | /' _---_~\
> `-)) )) ( |__>--<__| | /' / ~\`\
> ,/,'//( ( \__>--<__\ \ /' // ||
> ,( ( ((, )) ~-__>--<_~-_ ~--____---~' _/'/ /'
> `~/ )` ) ,/| ~-_~>--<_/-__ __-~ _/
> ._-~//( )/ )) ` ~~-'_/_/ /~~~~~~~__--~
> ;'( ')/ ,)( ~~~~~~~~~~
> ' ') '( (/
> ' ' `
> P A R M E D
>
> ParmEd: a Parameter file Editor
>
>
> ['parm.in']
> Reading actions from parm.in
>
> Adding prmtop ionicbox.prmtop to parm list. ionicbox.prmtop is the active
> parm.
> Residues :MTO are now considered to be solvent
> Setting MOLECULE properties of the prmtop (SOLVENT_POINTERS and
> ATOMS_PER_MOLECULE)
> Outputting Amber topology file ionicbox2.prmtop
> Done!
>
>
> =========================================md1.out
> =============================================
>
> -------------------------------------------------------
> Amber 12 SANDER 2012
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 12
>
> | Run on 03/20/2014 at 18:37:13
>
> [-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=10,
> &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 = 03/20/14 Time = 17:50:11
>
> | 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 = 10.00000, 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 = 462418
> 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= 10.000 Tol =0.100E-04
> Ewald Coefficient = 0.27511
> Interpolation order = 4
>
> | PMEMD ewald parallel performance parameters:
> | block_fft = 1
> | 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.
>
> [s.nasiri.chemcluster 22BMIBR256MTO_oack]$ more in
> -p ionicbox.prmtop
> checkValidity
> setMolecules ATOMS_PER_MOLECULE=true
>
> ==========================mdin.in
> ======================================================================
>
> &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=10,
> &end
>
>
> ============================ionicbox.pdb==========================================================
> more ionicbox.pdb
> HEADER
> TITLE Built with Packmol
> REMARK Packmol generated pdb file
> REMARK Home-Page: http://www.ime.unicamp.br/~martinez/packmol
> REMARK
> ATOM 1 C1 MTO A 1 18.138 0.459 16.198 1.00
> 0.00
> ATOM 2 H2 MTO A 1 18.179 1.448 16.337 1.00
> 0.00
> ATOM 3 H3 MTO A 1 17.328 0.231 15.656 1.00
> 0.00
> ATOM 4 H4 MTO A 1 18.085 0.000 17.086 1.00
> 0.00
> ATOM 5 O5 MTO A 1 19.370 0.004 15.474 1.00
> 0.00
> ATOM 6 H6 MTO A 1 20.178 0.233 16.015 1.00
> 0.00
> ATOM 7 C1 MTO A 2 3.004 13.078 24.333 1.00
> 0.00
> ATOM 8 H2 MTO A 2 3.588 13.763 24.768 1.00
> 0.00
> ATOM 9 H3 MTO A 2 3.173 13.073 23.347 1.00
> 0.00
> ATOM 10 H4 MTO A 2 2.044 13.302 24.505 1.00
> 0.00
> ATOM 11 O5 MTO A 2 3.310 11.725 24.902 1.00
> 0.00
> ATOM 12 H6 MTO A 2 3.143 11.731 25.886 1.00
> 0.00
> ATOM 13 C1 MTO A 3 22.981 17.655 29.035 1.00
> 0.00
> ATOM 14 H2 MTO A 3 23.051 17.908 29.999 1.00
> 0.00
> ATOM 15 H3 MTO A 3 22.702 16.697 28.961 1.00
> 0.00
> ATOM 16 H4 MTO A 3 23.870 17.778 28.592 1.00
> 0.00
> ATOM 17 O5 MTO A 3 21.963 18.526 28.362 1.00
> 0.00
> _______________________________________________
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Mar 20 2014 - 09:00:03 PDT
