[AMBER-Developers] Amoeba on sleap

From: MengJuei Hsieh <mengjueh.uci.edu>
Date: Fri, 04 Jun 2010 17:50:43 -0700


I am not sure if this is a place to ask for some advise, but here it is.

I was thinking about adding IONs into Amber's Amoeba force field, I thought
I can copy Amoeba ION parameters from
http://dasher.wustl.edu/tinker/distribution/params/ and add it to sleap's
amoebapro.prm and some libs. But I am hitting a wall and there seems to be
no detail documentation about getting a new parameter set anyway. There is
some other odd things like the amoeba parameters parser only accept the
atoms sequence start from 1, and the residue library seems to be asking for
a numerical atomtype.

Here is what I did, I created a MG.prm and MG2.off to be independent from
amoebapro.prm so that I can modify it easily.

% sleap
[gtkleap]$ loadoff MG2.off
[gtkleap]$ loadamoebaparams MG.prm
[gtkleap]$ desc MG2
UNIT name: MG2
R<MG2 1>
[gtkleap]$ desc MG2.1
A<Mg+ 1>
[gtkleap]$ desc MG2.1.Mg+
Name: Mg+
Type: 1
Charge: 2
Element: Mg
Atom position: 0 0 0
[gtkleap]$ saveamoebaparm MG2 test.top test.crd
Error: undefined numvec parameter pole of atom

I am not sure what I am missing, can someone help me out? :-)

Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine.

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Received on Fri Jun 04 2010 - 18:00:03 PDT
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