AMBER Archive (2008)

Subject: Re: AMBER: Problems with sleap and amoeba

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Aug 19 2008 - 18:51:18 CDT

> !entry.LAN.unit.atoms table str name str type int typex int resx int
> flags int seq int
> elmnt dbl chg
> "La1" "204" 0 1 17825795 1 57 3.000000

Note that the 1st 2 elements are "str name str type" == "La1" "204".

Therefore your atom type is "204" which is an atom number rather than the
name of a type. Normally there would be a type like La (or maybe La3 since
it's La+3), and the type would be defined in a frcmod file.

The format of amoeba.prm doesn't resemble anything from my experience of
earlier versions of amber; maybe there is more new in amber than I am
aware of (quite possible). Perhaps leap has been re-jiggered to allow
parms based on atom numbers from a seperately-loaded pdb, or you are mixing
conventions from another program.

Bill
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