Hello Colleagues,
I tried to run nmode to find the entropy contribution for a protein with 350
residues and it didn't work. I did energy minimization before running nmode
and it failed. Then I tried to use ntrun =4 in nmode input files and a
failure message "stop in nonbon1, npr=5950" showed up. I used 2 nmode input
files to try if any did work and a failure pop -up message appeared. Knowing
that I used mmpbsa.pl script to compute the binding energy. Any suggestion
or solution will be appreciated.
Here are the input files:
Minimization:
PIK: initial minimisation solvent + ions
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 5000,
ntx = 1,
ntb = 0,
ntr = 0,
cut = 10,
ntpr = 50,
drms = 0.0001,
&end
END
nmode input files: (I tried both of them but didn't work)
First file
Newton-Raphson minimization for kinase
&data
ntrun = 4, nsave=20, ndiag=2, cut=95.0, ibelly=0,icons=0,
nprint=1, ioseen=0,
drms = 0.001, maxcyc=10000, bdwnhl=0.1, dfpred = 0.1,
scnb=8.0, scee=2.0, idiel=0,
&end
Second File
Newton-Raphson minimization for 3HHM
&data
ntrun = 4, ntx=1, nsave=20, ndiag=2, cut=95.0, ibelly=0,
nprint=1, ioseen=0,icons=0,
drms = 0.0001, maxcyc=8000, bdwnhl=0.1,dfpred=0.01,
scnb=2.0, scee=2.0,dielc=1, idiel=1,ismem = 1,
&end
Regards,
Dima Sabbah
PhD student
College of Pharmacy
University of Nebraska Medical Center
Omaha,NE
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 05 2010 - 09:30:02 PDT
