[AMBER] reduce

From: George Tzotzos <gtzotzos.me.com>
Date: Fri, 11 Jun 2010 11:03:02 +0200

I'm trying to run <reduce> and get the following error message

Processing file: "/Users/george1/Desktop/bom.pdb"
Database of HETATM connections: "/Users/george1/Programs/amber11/dat/reduce_wwPDB_het_dict.txt"
Processing only 'A' conformations.
VDW dot density = 16/A^2
Orientation penalty scale = 1 (100%)
Eliminate contacts within 3 bonds.
Ignore atoms with |occupancy| <= 0.01 during adjustments.
Waters ignored if B-Factor >= 40 or |occupancy| < 0.66
Aromatic rings in amino acids accept hydrogen bonds.
Building or keeping OH & SH Hydrogens.
Rotating NH3 Hydrogens.
Processing Met methyls.
ERROR CTab(/Users/george1/Programs/amber11/dat/reduce_wwPDB_het_dict.txt): could not open
*WARNING*: Res "BOM" not in HETATM Connection Database. Hydrogens not added.
Found 0 hydrogens (0 hets)
Standardized 0 hydrogens (0 hets)
Added 0 hydrogens (0 hets)
Removed 0 hydrogens (0 hets)

The strange thing is that I have no amber11 sub-directory.

g:~ george1$ echo $AMBERHOME

amber11 was re-named amber11_parallel

Any suggestions?

Many thanks


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Received on Fri Jun 11 2010 - 02:30:07 PDT
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