On Tue, Feb 21, 2012, Beale, John wrote:
>
> The PDB file that I loaded into LEAP possessed charges for each of
> its atoms. I did a "savepdb" from LEAP and the new PDB file contained
> no charges. Is this normal behavior for LEAP, or have I now lost my
> charges?
"Real" PDB files don't have charge information, and LEaP doesn't expect to
find any, nor to make use of it. You could use a mol2 file rather than a PDB
file to get charges into LEaP.
You don't say what you are trying to do, or why you have (or want to have)
charges in your PDB files. So it's hard to give good advice, but note that
the "-pqr" option to ambpdb will create so-called PQR files, which look at lot
like PDB files, but have extra radius and charge information in them. Such a
format is often used of Poission-Boltzmann and related calculations. But I'm
really just guessing here.
...dac
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Received on Tue Feb 21 2012 - 05:30:03 PST
