Dear David,
This makes sense, but then it raises another question, how to objectively
decide these atom types (nomenclature).
Can you please suggest a scheme/technique for example to assign unique atom
types to one of the two redox states of the Heme cofactor?
I think these will have to be also different from any of the standard AA,
nucleic acid, Water, and ion atom types. Thus I'm not sure how to approach
this.
Looking forward to your valuable feedback and suggestions.
Thank you very much and best regards.
Vaibhav
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
https://niperguwahati.ac.in/DOC/profile/dixit.pdf
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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On Wed, Dec 21, 2022 at 7:32 PM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Dec 21, 2022, Vaibhav Dixit via AMBER wrote:
>
> >> Thank you for your earlier suggestions with FeS cluster which worked.
> >> But I'm running into errors while trying to parameterize a protein that
> >> contains 2-redox states of the same cofactor
>
> If you have two cofactors that are really different (e.g. they are in
> different redox states, and hence have different charges and force field
> parameters), then you have to give them different names, and different atom
> types (if the bonding info is different).
>
> I don't know of any way to do this automatically, but I'm not an MCPB
> person. But I'm guessing you need to manually edit the files for one of
> the
> two cofactors, so that it can be distinguished from the first.
>
> ....dac
>
>
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Received on Wed Dec 21 2022 - 06:30:04 PST
