From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Tue Apr 28 2009 - 11:19:58 CDT
Hi Dimitry, it depends on where you use an atom index within NAMD.
Usually numbers starting from 1 are read.
You don't need to apply the offset manually, though: [$A get serial]
in VMD will give you the 1-based numbers.
Giacomo
---- -----
Giacomo Fiorin
Center for Molecular Modeling at
University of Pennsylvania
231 S 34th Street, Philadelphia, PA 19104-6323
phone: (+1)-215-573-4773
fax: (+1)-215-573-6233
mobile: (+1)-267-324-7676
mail: giacomo.fiorin_<at>_gmail.com
web: http://www.cmm.upenn.edu/
---- ----
On Tue, Apr 28, 2009 at 9:40 AM, DimitryASuplatov <genesup_at_gmail.com> wrote:
> Hello,
>
> I`ve noted that [$A get index] in vmd gives out the index sequence
> starting from 0 while pdb and psf numeration starts from 1.
>
> Does NAMD treat this correctly or should I apply offset manually?
>
> Thanks,
> SDA
>
>
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