Hi
On Thu, Mar 10, 2016 at 8:45 PM, Robert Molt <rwmolt07.gmail.com> wrote:
> Good evening,
>
> I am somewhat confused on execution; I am having trouble reconciling the
> manual and the example. In the example given, it seems like one is using
> a Linux command (import) in csh rather than bash, as if one is doing
> this on the command line. If so, why is Amber being defined as a
> variable on the next line? I do not see "import" as a command in the
> manual under parmed, so I assume this not meant to be done within the
> ParmEd interface? Or perhaps this is written in Python, and this is the
> use of "import?" I'm not familiar with Python so I am unsure.
>
>
I am sorry for the confusion. I don't think AT15 supports conversion from
amber to gromacs. So I suggested to use developing version of ParmEd.
The commands I sent are Python code.
First, you need to install developing version of ParmEd from pip:
*pip install
https://github.com/ParmEd/ParmEd/archive/2.0.5.tar.gz
<
https://github.com/ParmEd/ParmEd/archive/2.0.5.tar.gz>*
After successfully install ParmEd, you create a file name your_script.py
with the command I sent.
then run in shell: *python your_script.py *(should be similiar as using
cpptraj)
> Is it possible to just enter a series of commands a la stdin being read
> into parmed.py
I think this is in todo list: https://github.com/ParmEd/ParmEd/issues/341
I do not see a command in the manual under parmed that
> seems associated with an output of a different file type? parmout just
> says to print out the revised topology file after given commands; it's
> not obvious to me if a command corresponds to this. I would guess not,
> given that the above example does not take this route?
>
>
yeah, the conversion is not existing in release version yet.
Hai
> On 3/10/16 4:13 PM, Hai Nguyen wrote:
> > Hi,
> >
> > For topology conversion, it would be best to use ParmEd to do that
> >
> > Jason made an example here:
> > https://github.com/ParmEd/ParmEd/issues/631 (required
> > develop version of ParmEd)
> >
> > Just curious: what type of analysis that AMBER does not offer (so we can
> > add more function if possible).
> >
> > Hai
> >
> > import parmed as pmd
> >
> > amber = pmd.load_file('prmtop', 'inpcrd')
> > # Save a GROMACS topology and GRO file
> > amber.save('gromacs.top')
> > amber.save('gromacs.gro')
> >
> >
> > On Thu, Mar 10, 2016 at 3:55 PM, Robert Molt <rwmolt07.gmail.com> wrote:
> >
> >> Good afternoon,
> >>
> >> I would like to convert my data into the GROMACS file type because I
> >> need to use an analysis tool only written for GROMACS. It's easy enough
> >> to convert a trajectory file in cpptraj:
> >>
> >> parm piggy.prmtop
> >> trajin full_no_waters.mdcrd 1 last 1
> >> autoimage
> >> trajout gromacs.trr trr
> >> go
> >> quit
> >>
> >> It does not seem, from the options in the manual, that cpptraj has a way
> >> to produce an associated parameter file in the GROMACS format. This
> >> confuses me, because I am unsure what good a GROMACS trajectory would be
> >> without the associated topology file. Under parmwrite, the manual seems
> >> to imply that one can select an alternative format for the parameter
> >> file (but the manual gives no examples of what formats are possible). Is
> >> it possible to convert Amber topology files to GROMACS style using the
> >> parmwrite keyword in cpptraj?
> >>
> >>
> >> _______________________________________________
> >> 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
>
> --
> Dr. Robert Molt Jr.
> r.molt.chemical.physics.gmail.com
>
>
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Received on Thu Mar 10 2016 - 20:00:03 PST
