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.
Is it possible to just enter a series of commands a la stdin being read
into parmed.py? 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?
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?
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
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Received on Thu Mar 10 2016 - 18:00:03 PST
