AMBER Archive (2006)

Subject: Re: AMBER: how to use AddPdbAtomMap

From: David A. Case (case_at_scripps.edu)
Date: Thu Aug 24 2006 - 17:47:50 CDT

On Thu, Aug 24, 2006, sethl_at_gatech.edu wrote:
>
> If the pdb file of interest is simply not just a 1->1 mapping of different
> names, how would I either convert this file to a leap recognized pdb file

Sounds like you need to think about manually editing the file, and/or writing
your own script. If there is not a 1->1 mapping between the atom names you
have and those you want, this would be a fairly unusual situation: you must
either have 2 or more names in your file that should be mapped to one in
Amber/IUPAC (the AtomMap function could do this), or you have a common name in
your file that should be split (depending on environment?) into two names for
the Amber/IUPAC conventions. [Offhand, that suggests a badly-constructed PDB
file.]

Maybe you could use AtomMap to do 95% of the conversion, and tackle the rest
by hand.

...dac

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