From: Richard Swenson (swenson_at_hec.utah.edu)
Date: Fri Nov 16 2007 - 14:45:02 CST
Ilya,
The CHARMM documentation website is found at:
http://www.charmm.org/document/Charmm/
Parmfile.doc explains parameter files.
Io.doc contains information about rtf files which are topology files.
As for the difference between the IC table and the definitions in the
parameter file, I'll explain what I think I know, and hope others will feel
free to correct me. The IC table is a matrix that the CHARMM program
creates that is full of bond data such as angles, dihedrals, bond lengths,
etc. This table is used by several commands in various different ways. For
example: if you wanted to build a lipid without any atom position data, and
you had a full IC table, you could use IC Build, and a couple other
commands, to generate coordinates from scratch! The IC table in the
TOPOLOGY file can be used to fill an empty IC table in CHARMM so that you
can build a molecule without any initial coordinates, however, during
dynamics, bond information and constants are taken from the parameter file.
In short, the IC table is used to build structures and manipulate
coordinates, while the parameter file data is used in minimization and
dynamics.
Hope this helps,
Richard
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Ilya Chorny
Sent: Friday, November 16, 2007 12:32 PM
To: Richard Wood
Cc: NAMD list
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
topology files.
I still do not understand the difference between the internal
coordinates and the definitions in the par files.
Thanks,
Ilya
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
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 55414-2959rwoodphd_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 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 pen pal. Text or chat with friends inside Yahoo! Mail. See
how.
-- Ilya Chorny Ph.D.
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