AMBER Archive (2009)

Subject: [AMBER] Problem with running anal module in amber

From: moitrayee_at_mbu.iisc.ernet.in
Date: Wed Oct 21 2009 - 01:47:17 CDT

Dear Amber Users,

I trying to obtain the pairwise interaction energies in a structure using the
anal module in Amber. Below I have pasted a sample anal.in file for my run.

decompose energies of protein
    1 0 0 0 560 1
    0 0.0 0.0 0.0 0.0
    1 0 0 0 0 1
    9.0 2.0 1.2 1.0
    1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
IOPT'ENERGY'
Receptor
RES 1 560
END
END
STOP

I run it as : anal -i anal.in -o anal.out -p 2zni_2yly.prmtop -c 2zni_2yly.prmcrd
where 2zni_2yly.prmtop is my topology file and 2zni_2yly.prmcrd is my inpcrd file.

The output I get is as follows:

          ---------------------------------------------------------------
          Amber 5.0 ANAL: Static Analysis for Energy/Structure UCSF 1997
          ---------------------------------------------------------------

   1. RESOURCE USE:

| New format PARM file being parsed.
| Version = 1.000 Date = 09/04/08 Time = 11:12:56

     Hollerith memory requirement of: 0 exceeds MAXHOL of 100000

It seems the residues in the protein are not recognized at all.
Please help me with your valuable suggestions.

Thanks a lot in advance.

Sincere Regards,
Moitrayee Bhattacharyya
Molecular Biophysics Unit
Indian Institute of Science
Bangalore-560012
India 

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