psfgen tyrosine anion-Fe bond

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 : Mon Dec 31 2012 - 23:21:23 CST