Dear Daniel Roe
Thanks for your help. I did the mentioned commands in the last topic, but
there were some errors. Also in the cpptraj step is the prmtop file was
written again or not?
I bring two simulation result. In the first number of atom was absent in
the incprd file, then I add number of atom and run again but...?
==================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
> 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 trajectory, 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.
>
========================running======================================================
mpirun -np 4 sander.MPI -O -i mdin -o min.out -p ionicbox.prmtop -c
ionicbox2.inpcrd -r min.x -x min.nc -e min.dat
=================================mdin===============================================
minimization
&cntrl
imin=1, ntpr=1000, ntwx=1000, maxcyc=10000,
ntb=1,
&end
1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| Run on 03/10/2014 at 10:16:46
[-O]verwriting output
File Assignments:
| MDIN:
mdin
| MDOUT:
min.out
|INPCRD:
ionicbox2.inpcrd
| PARM:
ionicbox.prmtop
|RESTRT:
min.x
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
min.dat
| MDCRD: min.nc
|MDINFO:
mdinfo
| MTMD:
mtmd
|INPDIP:
inpdip
|RSTDIP:
rstdip
|INPTRA:
inptraj
|
Here is the input file:
minimization
&cntrl
imin=1, ntpr=1000, ntwx=1000,
maxcyc=10000,
ntb=1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
ERROR: I could not find the number of atoms or the time on
the second line of your inpcrd file [ionicbox2.inpcrd]. Bad INPCRD
file!
=====================================================================================
****************************I add number of atoms by hand and run
again**************************************************
2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| Run on 03/10/2014 at 10:16:01
[-O]verwriting output
File Assignments:
| MDIN:
mdin
| MDOUT:
min.out
|INPCRD:
ionicbox2.inpcrd
| PARM:
ionicbox.prmtop
|RESTRT:
min.x
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
min.dat
| MDCRD: min.nc
|MDINFO:
mdinfo
| MTMD:
mtmd
|INPDIP:
inpdip
|RSTDIP:
rstdip
|INPTRA:
inptraj
|
Here is the input file:
minimization
&cntrl
imin=1, ntpr=1000, ntwx=1000,
maxcyc=10000,
ntb=1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
ERROR: Problem reading coordinates or velocities from ionicbox2.inpcrd
I could not understand line 3 :
17.155 0.887 16.111 17.196 1.876 16.250 16.345 0.659 15.569
17.102
========================ionicbox2.inpcrd==============================
Cpptraj Generated
trajectory
17.155 0.887 16.111 17.196 1.876 16.250 16.345 0.659 15.569
17.102
0.428 16.999 18.387 0.432 15.387 19.195 0.661 15.928 2.021
13.506
24.246 2.605 14.191 24.681 2.190 13.501 23.260 1.061 13.730
24.418
2.327 12.153 24.815 2.160 12.159 25.799 21.998 18.083 28.948
22.068
18.336 29.912 21.719 17.125 28.874 22.887 18.206 28.505 20.980
18.954
28.275 21.259 19.911 28.350 16.623 19.816 0.461 15.834 19.474
-0.048
17.456 19.659 -0.070 16.690 19.334 1.335 16.459 21.285 0.712
15.627
21.441 1.242 5.497 18.154 18.633 6.147 18.338 17.896 5.103
17.242
18.510 4.767 18.838 18.612 6.206 18.220 19.953 6.600 19.130
20.074
...
21.413 17.158 11.520 22.189 16.281 12.029 21.296 15.188 12.942
22.067
14.284 13.436 21.164 13.192 7.013 21.510 19.599 14.043 21.676
12.584
7.511 20.483 17.126 9.640 20.063 15.884 10.078 23.235 18.023
12.443
22.835 13.881 13.720 22.414 14.809 13.935 20.397 13.595 12.657
20.818
12.670 12.527 20.528 15.590 11.255 20.948 14.658 12.288 22.527
16.824
11.032 22.962 15.876 8.485 21.049 20.131 8.074 22.629 20.134
10.653
19.723 19.663
29.999 30.000 29.983
==============================================================
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Received on Mon Mar 10 2014 - 00:30:03 PDT
