AMBER Archive (2008)

Subject: Re: AMBER: Problems with sleap and amoeba

From: Neil J. Henson (neil.henson_at_lanl.gov)
Date: Tue Aug 19 2008 - 19:03:52 CDT

Bill,

Thanks for the reply.

My understanding is that support for the amoeba potential form has only
recently been added to the code in a user-friendly manner in Amber10. The
amoeba.prm is part of the AMBER distribution
($AMBERHOME/dat/leap/gleap/amoeba.prm) and I took the format for the lib
file from $AMBERHOME/dat/leap/gleap/amoeba_wat.off which does indeed have
the atom type number in that field. It seemed strange to me also, but it
seems to work just fine for the examples in $AMBERHOME/test/sleap/amoeba.
Although those examples don't have anything exotic like lanthanum of
course :-) .

Neil.

>> !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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