[AMBER] bond missing in phosphate group after antechamber run

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From: Krisztina Feher <feher_krisztina.yahoo.com>
Date: Wed, 7 Nov 2012 11:00:38 -0800 (PST)

Hi,

I am trying to derive GAFF parameters for a modified DNA residue with antechamber. I capped the residue with H's and ran through antechamber and parmcheck without error. However the bond between the oxigen and phosphorus is missing in the mol2 file as well as the respective parameters in the .frcmod file. Could someone have a look at teh input pdb file for antechamber to figure out the reason for this?

Thanks in advance,
Krisztina

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X-unknown/x-pdb attachment: THis_ver9.pdb

Received on Wed Nov 07 2012 - 11:30:02 PST