Dear Jacob,
What do you want to get after geometry optimization of such a
molecular system? I mean such a _large_ & _multiply charged_ molecule:
The conformation generated after geometry optimization (even in case
of success) for sure will not be representative...
Personally, I would use the R.E.D. tools or R.E.D. Server (see
http://q4md-forcefieldtools.org/), and split this large molecule into
well characterized building blocks. You can find many examples of this
approach in R.E.DD.B:
See for instance: http://q4md-forcefieldtools.org/REDDB/projects/F-90/ :
"The building block approach presents the following advantages over
the whole molecule approach: (i) the cpu time required for geometry
optimization and molecular electrostatic potential (MEP) computation
is drastically decreased, (ii) the optimized geometry of the
conformation(s) of each building block is fully defined and
controlled, (iii) conformations not suited for charge derivation,
presenting non-bonded interactions only observed in gas phase geometry
optimization are discarded, (iv) cofactors and their analogs are
simultaneously involved in a single and highly homogenous approach,
and finally (v) by generating averaged charge values for connecting
groups, additional and highly compatible charge derivation procedures
can be performed for an infinity of new cofactor analogs constituting
"add-ons" to the present R.E.DD.B. project"
See also the work of Guo et al:
http://pubs.rsc.org/en/Content/ArticleLanding/2012/CC/c2cc36546d
These authors used R.E.D. to derive MEP-based charges for a heparan
like molecule.
regards, Francois
> When I run antechamber for a specific molecule, it throws a seg fault after
> sqm finishes. The molecule is large at 184 atoms, and has a -8 charge, but
> this should not be an issue once calculations are completed. A similar
> problem was mentioned in the
> archive<http://archive.ambermd.org/201101/0383.html>,
> but there was no clear solution. The file in question is partially
> written, then the seg fault always occurs during writing of the same
> line/atom. I logged cpu and memory usage, but nothing strange seems to be
> happening. Has anyone dealt with this problem before? Would it be
> possible to use the information in sqm.out to manually create the necessary
> output file? It is likely an error somewhere on my end, but I am not sure
> how to go about debugging at this point and am not familiar with amber file
> formats. Any suggestions would be very much appreciated.
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Received on Fri May 24 2013 - 00:00:02 PDT
