Re: AMBER: Use of ibelly with nmode analysis

From: marti <>
Date: Thu, 24 Feb 2005 12:47:28 +0100

I have recently found the same problem.
One solution is just that to use LOWERCASES for the keywords res ,end ,
atom etc.
Alternatively one should modify the data statements at the top of the
rgroup.f file in the $AMBERHOME/src/nmode directory and recompile nmode.


From: <

Date: Tue Jul 13 2004 - 14:30:30 BST

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:

 ntrun=1, ibelly=1,
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

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

Any help would be grately appreciated

Many thanks

Prof. Adriano Martinelli
Dip. Scienze Farmaceutiche
Via Bonanno, 6
56126 PISA
Tel ++39 050 2219556
Fax ++39 050 2219605
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Received on Thu Feb 24 2005 - 11:53:00 PST
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