difficulties using SMD on atoms in large systems

From: Philip Blood (philb_at_hec.utah.edu)
Date: Tue Oct 04 2005 - 12:42:01 CDT

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Hi,

I am running NAMD 2.5 and SMD will not work on any atom which has an
index that cannot fit in a PDB file (i.e. index greater than 99999). It
does not recognize that these atoms have been tagged for SMD in the
occupancy column and gives the error :

FATAL ERROR: SMDFile contained no SMD atoms (atoms w/ nonzero occupancy)

Is there any workaround for this other than recreating my structure file
so that the atoms of interest show up in the first 99999 atoms (I have
done this previously to workaround this problem, but I would prefer not
to do it again). Has this issue been fixed in newer versions of NAMD?

Thanks,
Phil Blood

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