Dear all users.
I have a few questions.
I use Amber11 and Ambertools1.4 based on cygwin at Window7. In Ambertools, I have simulated normal mode calculation using NAB. Under the same conditions, I have conducted nmode calculation using MMPBSA in Amber11. When I compared obtained two types of energy, these are not matched. What reason does not match?
I send each of the input file and the topology file, PDB file used in the nab of nmode calculation.
PDB file was made by LMOD conformational search.
Topology file and coordinate file were created by below..
source leaprc.GLYCAM_06
set default write14scale on
a = loadpdb *.pdb
saveamberparm a *.prmtop *.inpcrd
quit
And what is the reason for the different Default of nmode of Amber11 and Ambertools? Especially why the default value of dielectric constant(dielc) is 4.0 ?
Have a good day.
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Received on Mon Sep 17 2012 - 23:30:02 PDT
