Hi,
I am not an expert in building parameters.
But I guess you have three options:
1) follow suggestions here
http://archive.ambermd.org/201310/0368.html
2) search literature on parameters for system similar to yours.
3) build your own parameters by performing QM calculations, at least
HF/6-31+g(d) level, on HEME-Fe-His system (you may choose only imidazole
ring of the HIS) and use RED server to build necessary files.
Hopefully somebody more experienced on the list will guide you in the right
direction.
On Sat, Jun 4, 2016 at 6:59 PM, 163邮箱 <zycz138.126.com> wrote:
>
> Hi,Vaibhav
>
> Thank you for your advice. But my heme group is attached to a His residue,
> so some parameters have still been missed. What should I do with that
> problem? The errors obtain are written below:
>
> Checking parameters for unit 'complex'.
> Checking for bond parameters.
> Could not find bond parameter for: NA - FE
> Checking for angle parameters.
> Could not find angle parameter: CW - NA - FE
> Could not find angle parameter: H - NA - FE
> Could not find angle parameter: NA - FE - NP
> Could not find angle parameter: NA - FE - NO
> Could not find angle parameter: NA - FE - NP
> Could not find angle parameter: NA - FE - NO
> Could not find angle parameter: CR - NA - FE
> There are missing parameters.
> check: Warnings: 13
> Unit is OK.
>
> Your sincerely,
>
> Allen Zou
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>
--
With Regards.
Dr. Vaibhav A. Dixit, (M.S. and Ph.D.: NIPER, Postdoc: AstraZeneca, UK and
IISc, Bangalore)
Associate Professor,
Department of Pharmaceutical Chemistry,
School of Pharmacy & Technology Management,
SVKM's NMIMS,
Mukesh Patel Technology Park
Babulde, Bank of Tapi River,
Mumbai-Agra Road,
Shirpur, Dist. Dhule -425405
India.
Email: vaibhav.dixit.nmims.edu
www.nmims.edu
http://pharmacy-shirpur.nmims.edu/faculty-and-research/faculty/dr-vaibhav-dixit/
+91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Sat Jun 04 2016 - 07:00:02 PDT
