From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Apr 01 2012 - 12:14:27 CDT
Sorry, I forgot to renumber HH. Now clean Fe-O.
fp
On Sun, Apr 1, 2012 at 7:03 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> 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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