nitu sharma wrote:
Dear Mark
After doing second step of inflategro i.e compression step
when I did the enery minimisation with nstep-10000 in parameter file
it terminated after 1547 steps and written that -
Converged to machine precision,
but not to the requested precision Fmax < 2000
Double precision normally gives you higher accuracy.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 1547 steps,
but did not reach the requested Fmax < 2000.
Potential Energy = 6.2109662e+05
Maximum force = 2.1254887e+04 on atom 6781
Norm of force = 7.1093488e+02
Can u suggest me probable solution of this problem .I am unable to
understand why this problem comes?
You have clashes in your system. Either the starting geometry of your protein
is bad, or you have incorrectly applied InflateGRO and still have protein-lipid
overlap. Look at your output structure, see which atom corresponds to number
6781, and see if you can tell where the problem is.
-Justin
Thanks a lot
Nitu Sharma
Structural biology lab
School of life Sciences
Jawaherlal Nehru University
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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