[AMBER] AMBER14 Tutorial: Lipid14 Edition

From: Shekter, Lee R <lshekter.bu.edu>
Date: Fri, 1 Aug 2014 18:03:58 +0000

I am using AMBER14, running on CentOS 6.4. I had an error which does not appear on the reflector list.

I followed the tutorial to the letter (except for the actual lipid, see below) and everything went smoothly up until the analysis part. I fed the input file into cpptraj using the following command as per the tutorial:

%cpptraj i box_dimension.cpptraj p DMPC_128.prmtop

(I made the lipid out of DMPC, rather than DOPC, since DMPC is biologically more relevant to me)

and this was the output:


CPPTRAJ: Trajectory Analysis. V14.05

    ___ ___ ___ ___

     | \/ | \/ | \/ |

    _|_/\_|_/\_|_/\_|_

Reading 'DMPC_128.prmtop' as Amber Topology

INPUT: Reading Input from file box_dimension.cpptraj

  [trajin 04_Hold_1.nc]

Reading '04_Hold_1.nc' as Amber NetCDF

  [trajin 04_Hold_2.nc]

Reading '04_Hold_2.nc' as Amber NetCDF

  [trajin 04_Hold_3.nc]

Reading '04_Hold_3.nc' as Amber NetCDF

  [trajin 04_Hold_4.nc]

Reading '04_Hold_4.nc' as Amber NetCDF

  [trajin 04_Hold_5.nc]

Reading '04_Hold_5.nc' as Amber NetCDF

  [trajin 04_Hold_6.nc]

Reading '04_Hold_6.nc' as Amber NetCDF

  [trajin 04_Hold_7.nc]

Reading '04_Hold_7.nc' as Amber NetCDF

  [trajin 04_Hold_8.nc]

Reading '04_Hold_8.nc' as Amber NetCDF

  [trajin 04_Hold_9.nc]

Reading '04_Hold_9.nc' as Amber NetCDF

  [trajin 04_Hold_10.nc]

Reading '04_Hold_10.nc' as Amber NetCDF

  [trajin 05_Prod.nc]

Reading '05_Prod.nc' as Amber NetCDF

  [vector test * box out vector.dat]

    VECTOR: Type Box, output to vector.dat

Error: [vector] Not all arguments handled: [ * ]

1 errors encountered reading input.

TIME: Total execution time: 0.1289 seconds.

There was no output. What does that error mean:
Error: [vector] Not all arguments handled: [ * ] ?

Thank you,

Lee Shekter
Boston University
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Received on Fri Aug 01 2014 - 11:30:02 PDT
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