AMBER Archive (2007)

Subject: Re: AMBER: regarding energy calculation

From: Abi Ghanem josephine (josephine.abighanem_at_ibpc.fr)
Date: Wed Sep 26 2007 - 04:13:38 CDT


gurpreet singh wrote:
>
> Hi Amber Users
>
> I am using ANAL module of AMBER 9 (although this has been explicitly
> omitted from the manual but it is still working )
>
> I made the following input file for Anal:
>
> ......................................................................
> &cntrl
> ntx=1,kform=1,ntb=+n,ntf=7,cut=10.0,imax=1,iopt=ENERGY
> &end
> .......................................................................
> But in the output file i am getting the following error, i think the
> error is because of something wrong in the input file,
> i am using Anal for the first time so please suggest me some way to
> rectify this error
> Also tell me if their is any online tutorial available for the Anal
> usage.
> .................................................................................
> 1. RESOURCE USE:
>
>
> rfree: Error decoding variable 1 2 from:
> &end
>
> this indicates that your input contains
>
> incorrect information
>
> field 1 was supposed to have
>
> a (1=character, 2=integer, 3=decimal) value
> ~
> ........................................................................................
>
>
>
>
> Thanks & Regards
>
> Gurpreet
Hi,
for the tutorial u can find it in the amber7 tutorial on the web page
of amber http://amber.scripps.edu/

ur input should look like this:
test of anal energies, compare to those from sander
    1 0 0 0 0 1
    0 0.0 0.0 0.0 0.0
    1 0 0 0 0 0
  99.0 2.0 1.2 1.0
    1 10.0 10.0 10.0 10.0 10.0 10.0 20.0 10.0 10.0
ENERGY
  first residue
RES 42
END
  second residue (or group of atoms)
ATOM 727 728 729 730 731
END
END
STOP

and then u run it with
$AMBERHOME/exe/anal -O -i analin -o analout -p test.prmtop -c test.inpcrd

hope it helps,
reagrds,
Josephine

-- 

Josephine ABI GHANEM IBPC, UPR 9080 13, rue P. et M. Curie, 75005 Paris, FRANCE

email: josephine.abighanem_at_ibpc.fr tel: 01 58 41 51 67 06 28 07 25 71

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