> My initial structure has a lot of clashes and problems (5.34 angstrom
> resolution obtained through cryo-EM). What I want to do is structural
> refinement using SGLD.
My usual solution to this issue, assuming there are not chains going
through rings, etc which are difficult to resolve, is to first perform a
minimization without electrostatics... The below is for explicit solvent,
so set igb/ntb to desired value and see if this works. This will remove
overlap of vdw but if high energy still remains, check for things like
backbone chains going through rings (PHE, TRP, ...) and try to resolve
them by hand. (Note that Chimera is freely available and is a nice
molecular graphics tool which atom selection syntax similar to CPPTRAJ
who borrowed the syntax from Midas/Chimera and extended it).
--tec3
min_noelec.in:
relax vdw
&cntrl
imin = 1, maxcyc = 300, ncyc = 300,
ntb = 2, ntp = 1,
cut = 9.0,
iwrap = 1,
lastist = 10000000,
lastrst = 10000000,
nmropt = 1,
&end
&wt
type = 'ELEC', value1 = 0.0,
&end
&wt
type = 'END',
&end
DISANG=inputs/restraints.in
LISTOUT=POUT
restraints.in:
&rst iat = 0, &end
> | Running AMBER/MPI version on 112 nodes
sander.MPI will likely not scale efficiently to 112 cores (although maybe
with GB); I would suggest trying on a single node or a couple of nodes
(for minimization) and it likely will be much faster. Minimization is not
well optimized/parallelized. If moving to production runs with PMEMD.mpi,
I recommend benchmarking across a series of nodes to see how scaling goes,
since if you are running less than 50% efficient, might as well run
multiple jobs at the same time.
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Received on Thu Jun 20 2019 - 09:30:02 PDT
