AMBER Archive (2004)

Subject: AMBER: Use of ibelly with nmode analysis

From: steven.j.enoch_at_gsk.com
Date: Tue Jul 13 2004 - 08:30:30 CDT

Amber users,

I am trying to perform normal mode analysis using the nmode module of
AMBER 8 on a protein-ligand complex using the ibelly function. Can
anybody tell me the syntax that I need to use to specify the residues I
want to include in the belly?

I have tried specifying them as follows:

&data
 ntrun=1, ibelly=1,
&end
--Belly
RES 1 10
RES 31 40
RES 42 42
RES 45 45
RES 64 64
RES 66 77
RES 93 100
RES 112 118
RES 124 124
END

and I get an error message saying 'rgroup: don't know what RES means'

Any help would be grately appreciated

Many thanks

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