Re: [AMBER] PDB file conversion server to meet the atom type requirement

From: case <>
Date: Sat, 7 Apr 2012 16:58:56 -0400

On Sat, Apr 07, 2012, Acoot Brett wrote:
> Is there a server for PDB file conversion in order to meet the atom type
> requirement of leap?

No conversion should be needed: Amber fully complies with the nomenclature
of the Protein Data Bank (version 3). [Any exceptions to this statement
will be treated as bugs.] PDB files with version 2 atom and residue names
should also be fully compatible with Amber, although this is not so well


(1) The above applies to the "modern" Amber force fields (ff10 and beyond).
Those that were created back when the PDB used version 2 still have
version 2 atom and residue names.

(2) Many programs create PDB-like files, but may have non-standard conventions
for atom and residue names. (CHARMM is a prominent example, but is by no means
unique.) If you get your PDB file from places other the, a
conversion to standard nomenclature may be required.

...good luck...dac

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Received on Sat Apr 07 2012 - 14:00:03 PDT
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