Dear Jason
Thanks for your help, but It seems that all problems are not solved,
because I faced with another error "ERROR: the combination ntb != 0, ntp
!= 0, ifbox == 0 is not supported! Input errors occurred. Terminating
execution."
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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Received on Thu Mar 20 2014 - 09:00:02 PDT
