Dear Jason Swails
Thanks for your quick replying. I did the commands and run minimization
step successfully, but in the simulation the "Error: Bad topology file. Sum
of ATOMS_PER_MOLECULE does not equal NATOM." was appeared. I don't know
what should I do?
Your Sincerely
Nasiri
===================================cpptraj============================================
cpptraj -p ionicbox.prmtop
CPPTRAJ: Trajectory Analysis. V13.22
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
AmberParm Title: [default_name]
Radius Set: modified Bondi radii (mbondi)
> trajin ionicbox.inpcrd
[ionicbox.inpcrd] contains 1 frames.
> fixatomorder outprefix fixed
FIXATOMORDER: Will attempt to fix atom ordering when atom numbering
in molecules is non-sequential.
Re-ordered topology will be output with prefix fixed
> trajout ionicbox2.inpcrd restart
> run
PARAMETER FILES:
0: ionicbox.prmtop, 1744 atoms, 264 res, box: Orthogonal, 272 mol, 1 frames
INPUT TRAJECTORIES:
0: [ionicbox.inpcrd] is an AMBER restart file, no velocities, Parm
ionicbox.prmtop (Orthogonal box) (reading 1 of 1)
Coordinate processing will occur on 1 frames.
REFERENCE COORDS:
No frames defined.
OUTPUT TRAJECTORIES:
[ionicbox2.inpcrd] is an AMBER restart file, Parm ionicbox.prmtop:
Writing 1 frames (1-Last, 1)
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM [ionicbox.prmtop] (1 actions):
0: [fixatomorder outprefix fixed]
Warning: ionicbox.prmtop already has molecule information. No reordering
will occur.
Warning: Setup failed for [fixatomorder outprefix fixed]: Skipping
----- [ionicbox.inpcrd] (1-1, 1) -----
100% Complete.
Read 1 frames and processed 1 frames.
ACTION OUTPUT:
DATASETS:
No data sets.
> quit
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
==============================md1.out==========================================
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 12
| Run on 03/11/2014 at 12:40:30
[-O]verwriting output
File Assignments:
| MDIN: mdin.in
| MDOUT:
md1.out
| INPCRD:
min.x
| PARM:
ionicbox.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 = 02/20/14 Time = 17:54:38
| 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 = 1 NMXRS = 26 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM.
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Received on Tue Mar 11 2014 - 02:30:02 PDT
