On Fri, Feb 05, 2010, Jim Miller wrote:
> >lyz=loadpdb model.pdb
> Loading PDB file: ./model.pdb
> Created a new atom named: HB1 within residue: .R<NLYS 1>
> Created a new atom named: HG1 within residue: .R<NLYS 1>
The atom names used in pdb files must match those in the Amber library.
Amber uses PDB version 3 nomenclature, but your input file is using an
older-style (version 2) set of atom names.
The simplest thing to do is to remove the hydrogens from your pdb file:
LEaP will build them back in with correct names.
If you really think the positions of the hydrogens in your input file are
important, you can use protonate (with the "-k" flag) to convert from old
style to new-style input. Or, use the reduce program shipped with AmberTools.
Or, google for other "remediation" programs offered by the RCSB that are
designed to handle this sort of conversion process.
...good luck....dac
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Received on Fri Feb 05 2010 - 04:30:03 PST
