On Mon, 2014-03-10 at 10:31 +0330, Saeed Nasiri wrote:
> 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
This will print ionicbox2.inpcrd as an ASCII mdcrd file, not an inpcrd
file. You need to add the keyword "restart" afterwards to get the
correct format (or change the suffix to ".rst7"). So this instead:
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 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
Apparently your topology file is fine.
[snip]
> --------------------------------------------------------------------------------
> 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!
This is because you printed out ionicbox2.inpcrd as a mdcrd file rather
than a restart. Adding the number of atoms on the second line will not
help (as you found out).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 10 2014 - 05:30:02 PDT
