On Tue, Jun 23, 2015 at 8:59 AM, Gerald Monard <
Gerald.Monard.univ-lorraine.fr> wrote:
> 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
>
In my (weak) defense, this is at least in the internal help (type 'help
parmwrite')...but it needs to be in the main manual as well, thanks for the
report.
> "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...
>
The only reason I use .parm7 is that it is the default extension used by
VMD to recognize an Amber topology (plus it's nice and unambiguous).
>
> 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
> >>
> >>
> >>
> ____________________________________________________________________________
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
>
> ____________________________________________________________________________
>
> 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
>
>
> ____________________________________________________________________________
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 23 2015 - 09:00:02 PDT
