From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Sun Sep 04 2011 - 14:17:38 CDT
I am trying to use AUTOPSFBUILDER from VMD to set a PLO2 patch between O2, Heme and His as described by Charmm topology file:
PRES PLO2 0.00 ! Patch residue for Heme ligand. Residues must be
! 1-O2 , 2-HEME , and 3-HIS
! O1 of the oxygen is bonded to the iron.
BOND 1O1 2FE
ANGLE 1O2 1O1 2FE 1O1 2FE 2NA 1O1 2FE 2NB
ANGLE 1O1 2FE 2NC 1O1 2FE 2ND
DIHE 1O2 1O1 2FE 2NA
IC 1O2 1O1 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1O2 1O1 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000
However AutoPsfBuilder only enables the patch between 2 residues.
How can I implement this patch using AutoPsfBuilder?
Thanks for any help.
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