AMBER Archive (2006)

Subject: Re: AMBER: amber atom type -> length of name

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 12 2006 - 01:59:48 CST

On Wed, Jan 11, 2006, Tim Meyer wrote:

> amber atom types are assigned to a 2-character string (CT, HN etc).
> however besides a warning from leap 3-character atom types seem to be read
> and understood correctly, am i wrong?

It would be good to know the answer here, even for 4-character atom types.
Does the code seem to read the parm.dat file correctly? That is what I
thought would have failed, but maybe not. If the prmtop file is created
correctly, you should be fine: the atom types are not really used in programs
like sander.

If you could figure out what is needed to make this work, that would be a
great help, especially for things like porting other force fields (e.g.
CHARMM) to Amber. But you do need to work with care, since atom types could
potentially be used in many places. Try changing one current type to a three
letter name, and then see if you can get identical energies before and after
the change.

...regards...dac

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