Sir,
I want to calculate binding energy of a nucleic acid ligand complex
(explicit simulation , TIP3Pbox) using mm_pbsa.pl script.
many values are explained for the input parameters
It would be helpful if you can suggest the appropriate values
* SCALE- lattice spacing in no of grids per angstrom. what value should i
choose?
* INP
*SURFTEN and SURFOFF
* IGB
*GBSA
i dont understand which values should i choose and its significance.
Also could i put MM= PB= GB= MS=1 to get binding energy without entropy and
then again run the program with NM=1 to get the entropy calculation?
It would be very helpful to get the needful suggestion.
thanking you
Mary Varughese
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Received on Tue Jul 23 2013 - 00:30:02 PDT
