Re: amber-developers: some new amber10 source directories

From: Michael Crowley <>
Date: Mon, 04 Dec 2006 10:21:55 -0800

Dave, should we put in a test case so others see how to run it?

David A. Case wrote:
> 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.
> ...regards...dac

Physical mail:   Dr. Michael F. Crowley
                  Department of Molecular Biology, TPC6
                  The Scripps Research Institute
                  10550 North Torrey Pines Road
                  La Jolla, California 92037
Electronic mail:
Telephone:         858/784-9290
Fax:               858/784-8688
Received on Wed Dec 06 2006 - 06:07:32 PST
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