Re: amber-developers: Name of Atom Types with more than 2 characters

From: David A. Case <>
Date: Fri, 8 Sep 2006 18:22:49 -0700

On Thu, Sep 07, 2006, Mengjuei Hsieh wrote:
> I am wondering that how many codes do I need to change the LEaP to accept
> atom type with more than two letters. Is there a way that I can estimate
> that?

Fortunately, the prmtop format itself allows up to four characters for the
atom type, so programs that read prmtop files might or might not need a lot of
change. Anything that reads or writes parmxx.dat or frcmod files is likely to
need changing, however. And all of this could include codes that others use
that are not even a part of Amber :-(.

Since there are 62 upper and lower case letters and digits, there are 62*62 =
3844 potential two-character atom types. Maybe we should consider that atom
types inside the program are just codes, and support some mapping between
these type-codes and human-readable (mnemonic) atom types.

Comments from others are welcome. Several times I have thought I would try to
change the two-character limit, but the practical steps to do that seem pretty

Received on Sun Sep 10 2006 - 06:07:27 PDT
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