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: [$A get serial]
in VMD will give you the 1-based numbers.
Center for Molecular Modeling at
University of Pennsylvania
231 S 34th Street, Philadelphia, PA 19104-6323
On Tue, Apr 28, 2009 at 9:40 AM, DimitryASuplatov <genesup_at_gmail.com> wrote:
> I`ve noted that [$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?
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