Hi.
OK, I've modified all my cpptraj scripts to add the amber keyword.
However, it would be nice to update the Amber manual (Table 29.2,
topology formats recognized by cpptraj) to be aware that topology files
ending by .top are supposedly recognized as Gromacs topology files. For
"my" files, cpptraj has changed its defaults value from previous
versions, since I've always named my Amber topology files as .top. I
guess I need to change this (bad?) habit...
Thanks,
Gerald.
On 06/23/2015 04:42 PM, Daniel Roe wrote:
> 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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--
____________________________________________________________________________
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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Received on Tue Jun 23 2015 - 08:30:03 PDT
