Coarse Graining setup question

From: Stefan Franzen (
Date: Tue Apr 26 2011 - 05:13:23 CDT

In the CG tutorial it states that you can eliminate null beads (beads with
zero mass) by rerunning the CG Builder. I tried this about 6 times without
success. I was able to build a PSF file by deleting the zero mass beads in
both the PDB and TOP files. However, I could not get further. I sent a
message a few minutes ago about a problem that may be related.
Specifically, the CG parameterization failed. Perhaps this is related to
the elimination of the zero mass bead. The issue is that there are missing
numbers in the PDB, PSF and TOP files because of the deletion of the zero
mass beads.

Stefan Franzen
Professor of Chemistry
North Carolina State University
Raleigh, NC 27695
Phone: 919-515-8915

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:02 CST