amber-developers: some new amber10 source directories

From: David A. Case <>
Date: Mon, 4 Dec 2006 09:09:13 -0800

Hi everyone:

You might be interested in a couple of new subdirectories in amber10:

amber10/src/reduce: This program adds hydrogens to proteins and nucleic
acids. It comes from Michael Word, and is pretty intelligent -- better than
what LEaP does in my view. I've modified it to use the IUPAC/Amber hydrogen
naming scheme. More information in README. I think we will be able to use
this to replace "protonate", and we might make this the standard way to
pre-process pdb files (of course, only after testing).

This program doesn't handle waters, so I'd love to merge in the capabilities
of gwh. Volunteers are welcome to pitch in.


amber10/src/sqm: "sqm" means "stand-alone quantum mechanics". This is code,
extracted by Mike and me from sander, that will carry out pure
semi-empirical or dftb calculations (no "mm" part). Right now, it just does
minimization, but this might be a starting point for a mopac replacement that
I hope we can (eventually) distribute both inside and outside of Amber.

I know that amber developers don't need no stinking documentation, so there
isn't any (yet). sqm.f is the driver program that just reads in the coords,
a namelist with options, and does the calculation. It's pretty raw right now,
but suggestions and improvements are welcome. It represents a "fork" from the
sander code, (so that bugfixes to sander will have to also be made to sqm),
but we couldn't see any real way to avoid that.

Received on Wed Dec 06 2006 - 06:07:31 PST
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