Re: +1 offset to VMD index file?

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
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:49 CST