From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Wed Mar 21 2012 - 11:34:47 CDT

Hello,

I have stumbled on a curious behavior of the autopsfgen extension while trying to cap the termini of a single amino acide residue.

I am capping the cterminus with CT3 and nterminus with NTER. The structure is then generated and it appears that 2/3 hydrogen atoms that are supposed be bound to the terminal nitrogen have been coopted into the CT3 cterminal cap.

This leads to a very strange structure as one might guess. I have tried doing separate steps of termini capping in different order and it appears that what ever the last patch residue is applied, it "steals" the hydrogen atoms from the previous patch step.

Does anyone know how to capture the psfgen commands that are being issued in the vmd extension so I can find out if it psfgens problem or it is just getting bad info from the extension gui.

Thanks
Brian