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
tested.
However:
(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 www.rcsb.org, 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
