[AMBER] the combination ntb != 0, ntp != 0, ifbox == 0 is not supported!

From: Saeed Nasiri <s.t.nasiri.gmail.com>
Date: Thu, 20 Mar 2014 19:01:10 +0330

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
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