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Lennard-Jones parameters

Qu Youxin qyx at IRIS.LSC.PKU.EDU.CN
Fri Mar 22 09:08:24 EST 1996

Dear X-PLORists,

I met the following  problems in my NMR structure calculations with X-PLOR, and I wish 
to have your kind help:

1. The parameter setting up for the Lennard-Jones 6-12 van der waals potential energy 
   calculations in protein NMR structures. In the manual of X-PLOR3.1, page 319-321, 
   an example in "refine_gentle.inp" is given as follows:

   >parameter                       {*Parameters for the repulsive energy term.*}
   >   nbonds
   >      tolerance=0.5 
   >      cutnb=11.5 ctonnb=9.5 ctofnb=10.5 tolerance=0.5 rdie vswitch switch
   >   end

   However, the example is used to refine DNA structures. Can the above parameters be 
   used in the case of protein structures or need some modification ? I wish someone 
   could send me a  set of " standard " parameters for protein.

2. Could anyone tell me how to set up different NOE scales for two NOE files in SA 

Any of your help is highly appreciated.


Youxing Qu
National Laboratory of Protein Engineering
and Plant Genetic Engineering
Life Sciences Center
College of Life Sciences
Peking University
Beijing  100871
P. R. China
E-mail:  qyx at IRIS.lsc.pku.edu.cn

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