Hello fellow Amber-lers,
I'm trying to simulate arrays of C2H2 zinc finger domains bound to DNA. My initial attempt using leap to make the Zn2+ failed as the ions escaped into the bulk solvent. My second approach was to use the 'Pang' method which uses four dummy atoms in a tetrahedral configuration to represent the charge presented to 2 Cys and 2 His. Unfortunately while the Cys stay coordinated to the zinc throughout my simulation, the His exhibit no attraction at all and the domain loses its structure as His drifts away. I used CYM and HID to achieve the required protonation state in the PDB file as zinc coordinates to the NE His atoms. For some reason leap would not recognise the HIN state outlined in Pang.
Anyone had any experience of this or can make any suggestions of why this is happening?
Grateful thanks!!
Mike
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Received on Wed Nov 20 2013 - 11:00:02 PST
