Re: [AMBER] Regarding the forcefield parameters for cytochrome P450 heme group

From: Vaibhav Dixit <>
Date: Sat, 29 May 2021 10:51:01 +0530

There are multiple ways to approach this problem and different methods have
been demonstrated in the tutorial for metal-ion modelling (link below).
You can try one of those and I guess you would have to use the same for the
Fe(II) state as well.
A comparison of the parameters thus generated with Shahrokh 2012 might help
you decide if these are reliable enough.
But the real test would be the comparison with existing experimental
spectroscopic, X-ray or high-level QM/MM data.

I hope this helps.

On Sat, May 29, 2021 at 1:09 AM Patil Pranita Uttamrao <> wrote:

> I would like to do the MD simulation of Cytochrome P450. For that, I got
> the heme group parameters for the pentacoordinate ferric(Fe(III)) complex
> which is in a high spin state from Shahrokh, Orendt, et al. 2012. However,
> I am unable to get the heme parameters for a native hexacoordinate
> ferric(Fe(III)) form which is in a low spin state. I would appreciate it
> very much if anyone can let me know, where can I get the low spin state(
> native hexacoordinate ferric form) parameters of the heme group in
> Cytochrome
> P450.
> Thanks in advance,
> Patil
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Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Received on Fri May 28 2021 - 22:30:02 PDT
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