[AMBER] Problem with formyl group parameters

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From: Carter M.K. <mkc1g09.soton.ac.uk>
Date: Mon, 18 Oct 2010 11:36:44 +0100

Hi,

I am studying QM/MM simulations at the University of Southampton and I am currently having a bit of trouble with antechamber not obtaining the correct parameters for certain compounds. All of these compounds contain formyl groups, which antechamber assigns incorrectly. Antechamber assigns the hydrogen of the formyl group as a h4 hydrogen. This cannot be the case as this atom type is for aromatic hydrogens with 4 electron withdrawing groups. I have attached an example molecule with its PDB, prepi and frcmod files. I think I am using the latest version so this is quite odd and I could use some help.

Thanks

Michael Carter

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chemical/x-pdb attachment: butyraldehyde.pdb

application/octet-stream attachment: butyraldehyde.frcmod

application/octet-stream attachment: butyraldehyde.prepi

Received on Mon Oct 18 2010 - 04:00:03 PDT