How to Amend a PBD file for NAMD

From: Zeinab Emami (zemami_at_ku.edu.tr)
Date: Wed Oct 01 2014 - 09:27:15 CDT

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Dear Namd-list Members,

I face a problem regularly. When I use a PBD file obtained from internet,
NAMD cannot read it an I get this error while producing the autopsf psf
file:

"Need to have at least one atom in your selection!"

I know the atom names and types and charges should be modified, though when
I tried to do it manually for a PDB file, I failed. I am wondering if
there is any automatic way to repair such a raw PDB file?

Thank you in advance and Best,
Zeinab

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