AMBER Archive (2004)

Subject: Re: AMBER: Use of ibelly with nmode analysis

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 13 2004 - 11:24:27 CDT

On Tue, Jul 13, 2004, steven.j.enoch_at_gsk.com wrote:
>
> 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'
>

Please post more of the output, so that we can see the exact message.
In particular, we need to see if the title to the section ("--Belly")
was recognized.

Also note that using the belly option with nmode is a very specialized
and limited option, that is, it is not simple to interpret the results you
will get.

...dac

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