Dear Matthew,
So did you keep both models the same? For consistency?
*"I’ve tried additional_resids, but this keyword only seems to add the side
chains of the additional residues. In an optimization, those side chains
will just fly away."*
I have the same problem and also the small model and the large model are
not the same.
While the large model is interconnected as it should be, in the small model
the molecules are independent of each other.
Thanks for your sharing. I will try it.
Best regards
Işılay
Vaibhav Dixit via AMBER <amber.ambermd.org>, 25 Eki 2022 Sal, 07:27
tarihinde şunu yazdı:
> Hi Matthew,
> Your procedure sounds like a smart trick (thanks for sharing). I'll try
> soon with some of the systems I'm working on.
> I'm curious to know more about your system since you mentioned about two
> metal ions.
> Is it like a FeS cluster system that contains two metal ions in the same
> redox-active metal center or do you have two metal centers each with a
> single metal ion?
> Earlier I faced challenges while setting up a system that contained two
> heme centers.
> Thus looking forward to learning from your experience.
> Thank you and best regards.
>
>
> 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
>
> Please consider the environment before printing this e-mail
>
>
> On Mon, Oct 24, 2022 at 8:35 PM Matthew Guberman-Pfeffer via AMBER <
> amber.ambermd.org> wrote:
>
> > Follow-up: For future reference, I was able to answer my own question by
> > coming up with the following procedure.
> >
> > 1) Edit the.fingerprint file generated by MCPB in the first step (-s 1)
> > for the standard (or small) model to have the same residues as the
> > fingerprint file for the large model. Also replace the standard model pdb
> > with the large model pdb (not sure if this is needed).
> >
> > 2) Run step 2 (-s 2)
> >
> > 3) Revert the fingerprint file for the standard model back to the
> original
> > version. (If this is not done, MCPB complains of mismatch residue names
> in
> > the database when assigning charges.)
> >
> > 4) Run step 3 and continue as normal from hereon out.
> >
> > This work-around leverages the fact that the bonded parameters and the
> > charges are derived independently by MCPB!
> >
> > Using this procedure, I got force constants and charges on the metal
> > centers (I have two metal ions) that fit the guidelines given in the MCPB
> > tutorial!
> >
> > Best,
> > Matthew
> >
> > > On Oct 23, 2022, at 6:26 PM, Matthew Guberman-Pfeffer <
> > matthew.guberman-pfeffer.uconn.edu> wrote:
> > >
> > > Dear AMBER community,
> > >
> > > The “small model” built by MCPB for my system undergoes a rearrangement
> > upon optimization that is not consistent with the crystal structure and
> > does not happen if I fully optimize the "large model” built by MCPB.
> > >
> > > Is it possible to have the small model be the same as the large model
> > for parameterization by MCPB? Or, to enlarge the small model to include
> the
> > extra groups found in the large model?
> > >
> > > I’ve tried additional_resids, but this keyword only seems to add the
> > side chains of the additional residues. In an optimization, those side
> > chains will just fly away. Is there a way to include the backbone of the
> > additional residues? (By additional, I’m thinking of including the
> > preceding and proceeding residue to the one that is coordinated.)
> > >
> > > Best,
> > > Matthew
> > >
> > >
> > >
> > >
> > >
> >
> >
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> >
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Received on Tue Oct 25 2022 - 04:00:03 PDT
