Dear Amber users,
I have a transition pathway(100 pdbs) from the inactive to active state of
my protein. After minimizing every structure of the pathway with the below
min.in file,
&cntrl
imin=1,
igb=5,
ntx=1,
ntpr=10,
ntb=0,
cut=999,
rgbmax=999,
maxcyc=10000, ntmin=1, ncyc=2000
I plotted the energy and ele and vdw terms from the min.out files, the
plots are attached. in conformation 73 and 74 I have a peak in ele and vdw
and in energy there is a decrease.How can I know what caused this changes?
and since the values are for the entire protein, do you have any
suggestions on how to find out what is happening residue wise?
Regards,
Maryam Irani
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Received on Mon Sep 22 2014 - 03:30:02 PDT
