[AMBER] Hybridization problem in Amber

From: Julian Stys <jstys.ualberta.ca>
Date: Fri, 25 Aug 2017 13:14:24 -0600


I am making a non-standard residue (Azide group attached to ALA residue),
and I'm using missing parameters from both gaff.dat and parm99.dat. For
nitrogens, I'm using (n1 14.01 0.530 Sp N), and so I added addAtomTypes{ {
"n1" "N" "sp" } } in my leaprc script.

The problem is that when I try to make the lib file, the hybridization
changes to sp2 because all the nitrogen types in leaprc.gaff are sp2. It
gives me the error: atom type n1 - unknown hybridization sp.

Does anyone know why the hybridization types are different in gaff.dat and
leaprc.gaff, and how I can fix the error when making the lib files? Thanks
in advance for your help!

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Received on Fri Aug 25 2017 - 12:30:02 PDT
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