[AMBER] GAFF atom type for CO

Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Krisztina Feher <feher_krisztina.yahoo.com>
Date: Thu, 20 Jun 2013 11:16:17 -0700 (PDT)

Hi,

I would like to assign GAFF atom types to diamino-pimelic acid (DAP) with Antechamber (see attahced pdb file), but the carbonyl carbons both on the backbone and on the sidechain as assigned "c2" atom types instead of "c". I embedded DAP in a tripeptide to derive the atom types and tried both sqm from version 12 and divcon from version 9, with sqm being worse (assigned "c1"). I tried "-j 5" option and used -nc 1 for the charge. Is there any way to force an atom type or what is it dependent on?

Thanks a lot!
Krisztina

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

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

Received on Thu Jun 20 2013 - 11:30:03 PDT