Dear Amber users,
Whenever I use the new sander with igb=3 for a distance-dependent
dielectric (in vacuo minimization), the minimization terminates
in "repeated linmin failure" after ~2500 steps, even though the
gradient is dropping gradually. For a system with no water, I use
500 steps of steepest-descent minimization followed by conjugate
gradient method. I have been setting ntb to 0 also. Here is a
sample input file:
&cntrl
imin = 1,
maxcyc = 5000,
ncyc = 500,
ntr = 0,
ntb = 0,
igb = 3,
&end
The system is a protein:DNA complex consisting of a 60 AA peptide and
an 8-b.p. DNA duplex.
Any suggestions would be appreciated. Thank you in advance for your help.
Sincerely,
Michael Cooney
Dept. of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602, USA
Received on Fri Sep 29 2000 - 07:49:07 PDT
