Re: solution for generating IC

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Feb 21 2009 - 18:26:13 CST

On Sun, 22 Feb 2009, CHINDEA Vlad wrote:

VC>
VC> Hi everybody
VC>
VC>
VC>

VC> Is there a free software available for transforming Cartesian
VC> coordinates into Internal Coordinates in the format required for
VC> CHARMM force field (IC statement) ? I guess CHARMM could do it but
VC> we do not have it and doing it manually it would be quite tediouse.

vlad,

i don't know the exact details of the format, but i would expect that it
should be scriptable with VMD. you can make a selection, translate it to
the origin and orient it, and then query the resulting coordinates, atom
type/names etc. and then use the information to write your internal
coordinate section with tcl (using printf style formatting with
"format").

cheers,
   axel.

VC>
VC>
VC>
VC> Many thanks and Best regards
VC>
VC> Vlad Chindea
VC>
VC> _________________________________________________________________
VC> Drag n’ drop—Get easy photo sharing with Windows Live™ Photos.
VC>
VC> http://www.microsoft.com/windows/windowslive/products/photos.aspx

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:21:45 CST