Hi,
This should've gone to the list... (isn't there an option "send
replies to list rather than to poster" to the mailing list?)
Tsjerk
On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> Hi Marius,
>
> You want iterate.
> You do have to make sure though that the numbering of your atoms in
> the structure file is correct. Than you can do:
>
> ndx=open("index.ndx","w")
> ndx.write("[ MyIndex ]\n")
> iterate selection, ndx.write("%d\n" % ID)
> ndx.close()
>
> I did make the assumption that you wanted the atom id's rather than
> the residue id's, since the latter are of no use to Gromacs.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Jun 27, 2008 at 1:17 PM, Marius Retegan
> <marius.s.rete...@gmail.com> wrote:
>> Hi All,
>> I'm using pymol to select (by residue) all the atoms around 10 angstroms
>> from a certain atom. Now I would like to write the residue id's of my
>> selection to an external file, so that I can integrated in the ndx file from
>> Gromacs. Do you have any idea how I could do that?
>>
>> Thanks,
>>
>> Marius Retegan
>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
