explict water models

Jiangsheng Jiang jiang at LAPLACE.CSB.YALE.EDU
Thu Aug 1 20:39:37 EST 1996


Paul Ramsland wrote:
> 
> I would like to set up a layer of explicitly defined waters around a protein
> model.  Could anyone tell me how to go about this using xplor.  Ideally I would
> like to have a 4-10 angstrom layer of water molecules and later set up a more
> relevant physiological buffer surrounding the protein.  Any advice will be
> greatly appreciated.
> 
> Regards Paul.
> 
> --
> Paul Ramsland BSc (Hon)
> 
> Immunobiology Unit
> Dept of Cell and Molecular Biology
> University of Technology, Sydney
> Westbourne St
> Gore Hill, NSW  2065
> Australia
> 
> Telephone: 61 2 9514 4045
> Facsimile: 61 2 9514 4095
> Email: paul at indy.bio.uts.edu.au
> Web Page: http://indy.bio.uts.edu.au/~paul/


See the script file "solref_radi.inp" in 

http://xplor.csb.yale.edu/~jiang/solvent_models

For example, the following lines:

   {* compute a solvent mask and store it in the map object "mask" *}
   declare name=mask domain=real end
   mask               
     average=false      { no ids in "protein" region       
}               
     mode=vdw           { use vdw radii                     }
     solrad=1.0         { a probe radius adds to vdw radii  }
     shrink=1.1         { the shrink radius (A)             }
     nshell=10          { the number of shells              }
     thick=1.0          { thickness (A) of the shell        }
     to=mask            { output to the mask map            }
   end

create a solvent mask with ten shells (layers) surrounding
protein. The first shell starts from the surface (approx. 2.0 angstrom
aparting from surface coordinates) and each shell has a thickness
of 1.0 angstrom; the last shell extends to the infinite.
The integers in the mask map indicate the number of the shell.

To write out the solvent mask:

   write map
     from=mask
     automatic=false
     extend=mole
     output="solvent_mask.map"
   end

However, the scripts run on the later X-PLOR versions than 3.1.


-- 
==================================================================
Jiansheng Jiang PhD          | Phone: (203) 432-5066            
Mol. Biophys. & Biochemistry | Fax:   (203) 432-3923            
Yale University              | mailto://jiang@laplace.csb.yale.edu
New Haven CT 06520-8114, USA | http://xplor.csb.yale.edu/~jiang  
==================================================================



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