From: E. Prabhu Raman (eraman_at_gmu.edu)
Date: Wed Aug 30 2006 - 16:19:46 CDT
I am trying to use NAMD to simulate a Coarse Grained model of protein(a polymer, which is an unbranched chain of beads).Thus,I have only C-alphas in my model.
I have prepared X-plor format parameter file and a .psf file. When I start my simulation in NAMD using these files, it stops and complains about having H-H bonds present.I found out that it is because I set the mass of C-alphas in my .psf file to 1.00. When I change it to 12.00, NAMD runs fine.
Is there any way in which I can set a mass of 1.00 for my C-alphas?
Ph.D Student,Bioinformatics & Computational Biology
George Mason University
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