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
   >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 
   refinement?

Any of your help is highly appreciated.

Youxing.

__________________________________________
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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