AMBER Archive (2002)

Subject: Charge export from Leap is rounded off

From: jeff dyason (j.dyason_at_mailbox.gu.edu.au)
Date: Sun May 26 2002 - 19:06:36 CDT

Hi,
        When I export a pdb file from Leap with the option "set default
pdbwritecharges on" the partial charges for each atom are output into
the pdb file in place of the structure factor for each atom. However,
the format for this field only allows 2 decimal places, where in most
cases the partial charge has 4 decimal places, leading to rounding
errors when the charge of each residue or in fact the whole protein is
summed for an external program. e.g. using the pdb file trx.pdb as
supplied in the tutorials gave a total charge of -4.0000 in Leap, but
when saved to a pdb file with the charges as outlined above the total
comes to -4.38.
        Can this be fixed by simply digging through the Leap source code,
finding the pdb export code and changing the format statement for the
partial charge from 2 decimal places to 4 ? Or is there something else
to consider ?

Thanks Jeff.
-----------
Jeff Dyason e-mail: J.Dyason_at_mailbox.gu.edu.au
Centre for Biomolecular Science and Drug Discovery
Griffith University (Gold Coast Campus)
        http://www.gu.edu.au/centre/cbsdd
PMB 50 Gold Coast Mail Centre Tel: +61 7 5552 7028
Queensland 9726 Australia Fax: +61 7 5552 8098