From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Thu Nov 15 2007 - 21:29:12 CST
IC stands for "Internal Coordinates", which are used to define bond lengths, bond angles, dihedrals and improper dihedrals. These are listed as part of each topology, and each dihedral must be defined, otherwise the energies will not be calculated correctly.
The .par file is the PARAMETER file, which tells you bond length, angle and dihedral values for various atom types. The topologies are read from the .inp file, so that each file is necessary. Just because something (ie, a dihedral) is listed in the topology file NAMD (or CHARMM) still requires a parameter file.
I'd recommend checking out www.charmm.org for documentation about the topology and parameter files.
Richard
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959
rwoodphd_at_yahoo.com
----- Original Message ----
From: Ilya Chorny <ichorny_at_gmail.com>
To: NAMD list <namd-l_at_ks.uiuc.edu>
Sent: Thursday, November 15, 2007 8:02:07 PM
Subject: namd-l: What is an IC table in the .inp files
Hi All,
I am working on porting a third party lipid forcefield to NAMD format.
When looking at the POPE forcefield in CHARMM27 (all_27***) there is a
something called an IC table which looks like a definition of dihedral
potentials. Is that correct? Also what is the relationship between the
.par and .inp files. Does NAMD default to the definition in the .inp
file prior to looking up up the values in the .par file. For example
if the IC table is the definition of the dihedral potential would namd
use those definitions and ignore what is in the .par file?
Thanks,
Ilya
--
Ilya Chorny Ph.D.
____________________________________________________________________________________
Be a better sports nut! Let your teams follow you
with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:33 CST