[AMBER] cpptraj error : not parsing mdvel file

From: Himanshu Joshi <himanshuphy87.gmail.com>
Date: Fri, 6 Jun 2014 16:30:17 +0530

Dear friends,

I tried cpptraj to convert an amber md velocity file from
binary (netcdf) to ascii format. It gave me the following error saying

*NETCDF Error: NetCDF: Variable not found...*

If anyone has any comment or suggestion regarding this,
please share with me.



*here are the details of the error output..*




cpptraj ../../parm/66_49nm_40.prmtop <ptraj.in

CPPTRAJ: Trajectory Analysis. V13.1
    ___ ___ ___ ___
     | \/ | \/ | \/ |
    _|_/\_|_/\_|_/\_|_
    AmberParm Title: [DEN]
    Radius Set: modified Bondi radii (mbondi)
INPUT: Reading Input from STDIN
  [trajin mdvel 1 10000]
    [mdvel] contains 10000 frames.
Warning: Box information present in parm but not in trajectory.
Warning: DISABLING BOX in parm [66_49nm_40.prmtop]!
  [trajout mdvel_asc.trj vel]

PARAMETER FILES:
 0: 66_49nm_40.prmtop, 171597 atoms, 55600 res, box: None, 55600 mol, 55599
solvent, 10000 frames

INPUT TRAJECTORIES:
 0: [mdvel] is a NetCDF AMBER trajectory containing velocities, Parm
66_49nm_40.prmtop (reading 10000 of 10000)
  Coordinate processing will occur on 10000 frames.

REFERENCE COORDS:
  No frames defined.

OUTPUT TRAJECTORIES:
  [mdvel_asc.trj] is an AMBER trajectory, Parm 66_49nm_40.prmtop: Writing
10000 frames (1-Last, 1)

BEGIN TRAJECTORY PROCESSING:
----- [mdvel] (1-10000, 1) -----
 0% NETCDF Error: NetCDF: Variable not found
Error: Getting frame 0

Read 0 frames and processed 0 frames.

ACTION OUTPUT:

DATASETS:
  No data sets.



Thanks
-- 
*With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
TheoryDepartment of Physics IISc.,Bangalore India 560012*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 06 2014 - 04:30:02 PDT
Custom Search