Hi,
If you change the file extension to '.parm7' or specify the 'amber' keyword
you will get an Amber topology. What is happening here is that basically
every format cpptraj knows about has a default file name extension
associated with it, which is what is used to determine the desired format
on writes (which is why you can specify just 'trajout traj.nc' now without
the 'netcdf' keyword and cpptraj knows you want a netcdf file). The
extensions I use for Amber and Gromacs topologies are '.parm7' and '.top'
respectively. It should be noted that only Amber topology writes are fully
supported by cpptraj - writes of other formats (like Charmm or Gromacs) are
suitable only for use in visualization or analysis (advanced topology
support is parmed's domain, and it does an outstanding job).
-Dan
On Tuesday, June 23, 2015, Gerald Monard <Gerald.Monard.univ-lorraine.fr>
wrote:
> Hello,
>
> I had a script that removed the box info in an Amber topology file.
> My script used cpptraj like this:
> cpptraj complex.top << END
> parmbox nobox
> parmwrite out complex.top
> END
>
> * With AmberTools13, I have the following results:
> CPPTRAJ: Trajectory Analysis. V13.0
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> AmberParm Title: [default_name]
> Radius Set: modified Bondi radii (mbondi)
> INPUT: Reading Input from STDIN
> [parmbox nobox]
> [parmwrite out complex.top]
> Writing parm 0 (complex.top) to Amber parm complex.top
> No trajectories loaded. Exiting.
>
> * With AmberTools15, I have the following results:
> CPPTRAJ: Trajectory Analysis. V15.00
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 06/23/15 14:12:49
> | Available memory: 28458 MB
>
> Reading 'complex.top' as Amber Topology
> INPUT: Reading Input from STDIN
> [parmbox nobox]
> Removing box information from parm 0:complex.top
> [parmwrite out complex.top]
> Writing topology 0 (complex.top) to 'complex.top' with format
> Gromacs Topology
> Error: writing topology file 'complex.top'
> 1 errors encountered reading input.
> TIME: Total execution time: 0.0386 seconds.
>
>
> With AmberTools15, there is an error because cpptraj wants to output a
> Gromacs topology(!). In the doc + in AmberTools13, the default parm
> format is Amber. Is this a bug?
>
> Thanks,
>
> Gerald.
>
> --
>
> ____________________________________________________________________________
>
> Prof. Gerald MONARD
> SRSMC, Université de Lorraine, CNRS
> Boulevard des Aiguillettes B.P. 70239
> F-54506 Vandoeuvre-les-Nancy, FRANCE
>
> e-mail : Gerald.Monard.univ-lorraine.fr
> tel. : +33 (0)383.684.381
> fax : +33 (0)383.684.371
> web : http://www.monard.info
>
>
> ____________________________________________________________________________
>
>
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>
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Received on Tue Jun 23 2015 - 08:00:03 PDT
