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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Received on Wed Oct 21 2009 - 00:30:02 PDT
