Dear Jason
Thanks for good commands, but I can't anything about fixatomorder. I did
the following things with cpptraj, but I don't know they are true or no? I
attached the new and old prmtop files but I can't write the coordinate file
(incprd).
Also this system is similar to amber ionic liquid simulation tutorial.
Your Sincerely
Nasiri
=================================================================================
cpptraj -p ionicbox.prmtop
CPPTRAJ: Trajectory Analysis. V13.22
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
AmberParm Title: [default_name]
Radius Set: modified Bondi radii (mbondi)
> fixatomorder
FIXATOMORDER: Will attempt to fix atom ordering when atom numbering
in molecules is non-sequential.
> parmwrite out ionicbox2.prmtop
Writing parm 0 (ionicbox.prmtop) to Amber parm ionicbox2.prmtop
> average ionicbox2.inpcrd
AVERAGE: Averaging over coordinates in mask [*]
Start: 1 Stop: Final frame
Writing averaged coords to [ionicbox2.inpcrd]
>
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Received on Sat Mar 08 2014 - 02:00:03 PST
