From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Apr 01 2012 - 09:53:13 CDT
Hi:
By using psfgen, I am trying to get iron(II) of heme bound to also the
para-O atom (OH) of tyrosine.
Starting from pdb with fully protonated tyrosine, what I get is Fe-H-O- bonding.
Removing the HH atom of tyrosine from pdb, no bond.
On stating "DELETE ATOM HH" in the patch, again no bond, while the HH
atom is added to the OH atom, irrespective of the protonation state of
tyrosine.
Thanks for pointing out what obvious I am overlooking.
The tentative patch is (don't pay attention to the partial charges)
GROUP !
ATOM 1CB CT2 -0.18 ! 1HD1 1HE1 uncoord -0.18
ATOM 1HB1 HA 0.09 ! | | 0.09
ATOM 1HB2 HA 0.09 ! 1HB1 1CD1--1CE1 0.09
GROUP ! | // \\
ATOM 1CG CA 0.00 ! -1CB--1CG 1CZ--1OH 0.00
GROUP ! | \ __ / \
ATOM 1CD1 CA -0.115 ! 1HB2 1CD2--1CE2 2FE- -0.115
ATOM 1HD1 HP 0.115 ! | | 0.115
GROUP ! 1HD2 1HE2
ATOM 1CE1 CA -0.115 ! -0.115
ATOM 1HE1 HP 0.115 ! 0.115
GROUP !
ATOM 1CZ CA 0.115 ! 0.115
ATOM 1OH OH1 -0.54 ! -0.51
GROUP !
ATOM 1CD2 CA -0.115 ! -0.115
ATOM 1HD2 HP 0.115 ! 0.115
GROUP !
ATOM 1CE2 CA -0.115 ! -0.115
ATOM HE2 HP 0.115 ! 0.115
DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND
DELETE ATOM HH
BOND 1OH 2FE
ANGLE 1CZ 1OH 2FE 1OH 2FE %NA 1OH 2FE 2NB 1OH 2FE 2NC
ANGLE 1OH 2FE 2ND
IC 1CZ 1OH 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1CZ 1OH 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1CZ 1OH 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1CZ 1OH 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1CZ 1OH 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000
francesco pietra
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:49 CST