Re: psfgen tyrosine anion-Fe bond

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Apr 01 2012 - 12:03:17 CDT

Partly solved. I.e., I had forgot to renumber the atoms in
relationship to the other ligands.

There is now Fe-O bond. However, that oxygen is also protonated, in
spite of starting from pdb TYR without HH and stating "DELETE ATOM HH"
in the patch.

Thanks for suggesting how to avoid that HH.

francesco pietra

On Sun, Apr 1, 2012 at 4:53 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> 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
>

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