From: Leonardo G. Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Wed Mar 29 2006 - 13:19:53 CST
On Wed, Mar 29, 2006 at 08:31:46PM +0800, xiaojing gong wrote:
> Hi,
> I mean that there is eight improper dihedrals needed to change name of atom type,
> IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163
> IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124
> IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121
> IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143
> IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143
> IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150
> IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065
> IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292
>
> BUT in the parmeter file, there is only NC2C X X C , so I am a little confused.
The IC entries in the topology file are not dihedrals, they are internal
coordinates that are used to guess the coordinates of atoms that might
be missing in your original structure. They are described in the NAMD
tutorial, please read the appendix that describes the topology file.
Leo
-- Leonardo Giantini Trabuco Ph.D. student Center for Biophysics and Computational Biology University of Illinois at Urbana-Champaign A: The answer comes first. Q: What's wrong with top-posting?
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