From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Fri Nov 16 2007 - 13:46:26 CST
For topology files, go to: http://www.charmm.org/document/Charmm/c32b2/rtop.htmlFor parameter files, go to: http://www.charmm.org/document/Charmm/c32b2/parmfile.html
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55419-2959
----- Original Message ----
From: Ilya Chorny <ichorny_at_gmail.com>
To: Richard Wood <rwoodphd_at_yahoo.com>
Cc: NAMD list <namd-l_at_ks.uiuc.edu>
Sent: Friday, November 16, 2007 1:31:44 PM
Subject: Re: namd-l: What is an IC table in the .inp files
Can you show me where in the Charmm website is the information on
I still do not understand the difference between the internal
coordinates and the definitions in the par files.
On Nov 15, 2007 7:29 PM, Richard Wood <rwoodphd_at_yahoo.com> wrote:
> IC stands for "Internal Coordinates", which are used to define bond
> bond angles, dihedrals and improper dihedrals. These are listed as
> each topology, and each dihedral must be defined, otherwise the
> will not be calculated correctly.
> The .par file is the PARAMETER file, which tells you bond length,
> dihedral values for various atom types. The topologies are read from
> .inp file, so that each file is necessary. Just because something
> dihedral) is listed in the topology file NAMD (or CHARMM) still
> parameter file.
> I'd recommend checking out www.charmm.org for documentation about the
> topology and parameter files.
> Richard L. Wood, Ph. D.
> University of Minnesota
> Dept. of Medicinal Chemistry,
> College of Pharmacy
> 717 Delaware St. SE
> Minneapolis, MN 55414-2959rwoodphd_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
> When looking at the POPE forcefield in CHARMM27 (all_27***) there is
> something called an IC table which looks like a definition of
> potentials. Is that correct? Also what is the relationship between
> .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
> use those definitions and ignore what is in the .par file?
> Ilya Chorny Ph.D.
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