Dear All,
I have a system with two carbohydrate molecules, each consists of four
residues. I basically want to turn off all the non bonded interactions
between these two molecules. For that, I use parmed with the following
command (after loading the original prmtop file)
addExclusions :1-4 :5-8
outparm new.prmtop
Then, I run a minimization with ntb=0 for both modified and unmodified
prmtop files. For both cases, in the mdout file I get exactly the same
energies, and the same total and local size of non-bond list (which is
10042). Non-bonded cutoff in minimization is 999A, so I was expecting to
have different energies. Apparently I am doing something wrong but not
sure what.
I am using AmberTools14. I also attach the prmtop files, if they might help.
Best,
Batuhan
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Received on Mon Apr 04 2016 - 03:00:03 PDT
