From: Alessandro Cembran (cembran_at_chem.umn.edu)
Date: Fri Nov 16 2007 - 14:23:08 CST
Ilya,
The internal coordinates have no influence at all on the energy or
forces, they are only needed (at least with CHARMM-the program) when you
want to build a residue from scratch or in a few other cases. Again,
they do not affect the connectivity or the structure. What matters is
the connectivity specified in the topology file (most important is BOND,
and ANGL and DIHE only when not using auto angl dihe). Once the
connectivity is specified, then the relative equilibrium values and
force constant are looked up in the parameter file. Those are the
numbers that have an influence on the energy and forces, forget about
the IC table. One important thing, if you are using lipids or residues
in general that need to be patched, always remember to "auto angl dihe"
right after the patch (this is for CHARMM-program, I guess there should
be something similar for NAMD psfgen) and put your water at the end
(most water models give raise to problems when auto angl dihe is in use,
so that's why you need to put the water at the end).
Hope this helps,
Alessandro
Ilya Chorny wrote:
> 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.
>>
>
>
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:33 CST