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#25711 10/31/10 04:23 PM
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G
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Dear all,
I am doing a simulation on Hemoglobin molecule.
In the topology file for Heme (toppar_all22_prot_heme.str), what is the difference between PHEM and FHEM.
I am little confused as to when the FHEM and PHEM has to be used.
For DEOXYHEMOGLOBIN, i am using only PHEM to pacth HEME to proximal Histidines.
Kindly let me know ...

Gurunath #25732 11/04/10 08:15 PM
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rmv Online Content
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The HEME stream file comments suggest--

FHEM; no ligand (His or gas) bound to Fe
PHEM; His bound to Fe
PLO2; His and O2 bound to Fe
PLIG; His and CO bound to Fe

The FHEM patch is needed to remove a couple N-Fe-N ANGLE terms added by (AUTO)GENERATE.


Rick Venable
computational chemist

rmv #27960 07/20/11 04:28 PM
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Hi rmv,
When FHEM is applied, the heme would be the free heme without any ligands? so Fe(2+) is only coordinated with four N atoms? I am not sure if I am correct? Please help.

Also is there parameter set for pentacoordinated Fe heme?
Thanks.

raylarry #27961 07/20/11 05:17 PM
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Technically, the PHEM patch produces a pentacoordinated Fe heme.

The HEME residue includes Fe bound to the 4 N atoms; the FHEM (Fix HEME) patch is needed as a correction, as noted above.


Rick Venable
computational chemist


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