Dear AMBER users,
In MM_PB/GB/SA analysis, I have problems with both un-reduced and
reduced complex approaches:
1) With the whole system, the igb=4 minimizations are too slow because
of
the large size of the protein. If I change to cut=16 from without
cutoff,
it converges much faster so I can use much fewer maxcyc.
But I don't know if it's a good choice because a) the energies are
different;
b) MM may be off quite a bit. Even if deltaG may not got affacted much
due to
cancelling-out, still std.dev. may be larger than it should be.
2) If I cut a reduced system out centered around the ligand, the new
complex
contains a lot of short pieces of individual peptide strands. The
re-creaction of
the receptor and complex prmtops introduces some new H in the
N-terminals and
new OXT in the C-terminals. These new atoms of course are not in the
original
snapshots taken out of MD trajectories. It looks that you cannot get a
prmtop
with leap without these new atoms because leap would complain the large
distances between the terminal atoms. I wonder how to get a workable
reduced
complex model.
Ant solution is welcome.
Thanks,
Chenglong Li
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Received on Wed Nov 19 2003 - 18:53:00 PST
