Thanks jason. It seems that the write frcmod in xprarmed.py does what I
want.
Thank you for your help
On Sun, Sep 14, 2014 at 5:03 PM, Arun Srikanth <askforarun.gmail.com> wrote:
> Thanks jason for the reply and the thanks for the great tool xparmed.py
> and parmed.py.
>
> The print dihedrals can be used to print the dihedrals that are defined
> between atoms. Is that right ?
> I have 53 atoms in the simulation. I am used the command in xparmed.py
> like .1-53. But what
>
> I would like to get isthe list of all the unique dihedraltypes that are
> defined. For example I want an output like this.
>
> X -NB-CU-X 1 0.000 180.000 3.000
> X -CU-SH-X 1 0.000 180.000 3.000
> X -CU-S -X 1 0.000 180.000 3.000
> X -CT-SH-X 3 1.000 0.000 3.000
>
> I am not sure how to to do this with parmed.py. Can you please help ?.
>
> Should I use readparm or any other command ?
>
> The reason I am asking this is I am creating a bond between two atoms. I need to know the new bond type, angle types and the dihedral types
>
> dhedral types that are to be defined.
>
> Thanks
>
> Arun
>
>
>
> On Sun, Sep 14, 2014 at 3:34 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>>
>>
>> > On Sep 14, 2014, at 2:47 PM, Arun Srikanth <askforarun.gmail.com>
>> wrote:
>> >
>> > Does any one how to get the dihedral types from the amber topology file.
>>
>> The printDihedrals command in ParmEd will do it.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sun Sep 14 2014 - 15:30:02 PDT
