Dear Matthew, David and the list.
I remember having tried this using HM1, HD1, FE1 and HM2, HD2 and FE2
residue names, but it gives weird geometry for one of the states after
minimization.
I think the parameters are wrongly assigned due to the replacement of force
constants and charges by the last-loaded frcmod and mol2 files.
I'm not an expert in the way these things are set in tleap, but I'm
assuming that parameters for the same atom types loaded from 1st
frcmod/mol2 files will be replaced by the 2nd ones.
David and other expert developers on the list might be able to confirm if
you are correct or my assumption is.
thank you for your valuable suggestions.
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 7:51 PM Matthew Guberman-Pfeffer <
matthew.guberman-pfeffer.uconn.edu> wrote:
> Playing on dac's suggestion, you can set the residue names for the
> oxidized and reduced hemes as HEO and HER, respectively. It’s then fine for
> the same atom types to be used, because they belong to different residue
> definitions.
>
> There are already oxidized and reduced (c-type) heme definitions in AMBER,
> and for either state, the residue name is HEH. I wonder how this issue is
> handled there. Check out the constant redox MD tutorial:
> https://ambermd.org/tutorials/advanced/tutorial33/
>
> It’s still unclear how, in my case, to handle this issue of two metal
> centers of the same element in different redox states within the same
> cofactor.
>
> Best,
> Matthew
>
>
> On Dec 21, 2022, at 9:02 AM, David A Case via AMBER <amber.ambermd.org>
> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> 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 - 07:00:02 PST
