From: Ilya Chorny (ichorny_at_gmail.com)
Date: Fri Nov 16 2007 - 13:31:44 CST
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.
>
>
>
> ________________________________
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-- Ilya Chorny Ph.D.
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