I think Adrian's recommendation is what I would do - use some large
positional restraints and release them slowly and hope the close distances
minimize out without exploding.
On Fri, Apr 24, 2026 at 12:29 PM ElBagoury, Abdulrahman Walid Attia Ibrahim
via AMBER <amber.ambermd.org> wrote:
> so what could be your recommendation ? is there a way to adjust for the
> close contacts ?
>
> Best,
> Abdulrahman
>
>
>
>
>
> Abdulrahman Walid Attia Ibrahim ElBagoury
> Antivirale und Antivirulenz-Wirkstoffe
>
> Helmholtz-Institut für Pharmazeutische Forschung Saarland
>
> University Campus E8.1, 66123 Saarbrücken
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>
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> ________________________________
> From: Adrian Roitberg via AMBER <amber.ambermd.org>
> Sent: Friday, April 24, 2026 5:59 PM
> To: ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER
> Subject: [EXTERN] Re: [AMBER] Need help in proceeding with md sim
>
> I know nothing about pdbfixer, but by the looks of it, there seemed to
> have done quite a bit of work trying to make sure there are no close
> contacts between residues, etc.
>
> Now, tleap is telling you that there are some serious close contacts.
>
> So, either pdbfixer did not do a good job, or it did, but then when you
> use reduce, the hydrogens mess things up.
>
> I am not sure if you can start your minimization with these coordinates,
> some of the contacts are too close.
>
> If you do minimize, you need to use some big restraints and let them go
> slowly.
>
> Adrian
>
>
> On 4/24/26 11:05 AM, ElBagoury, Abdulrahman Walid Attia Ibrahim via
> AMBER wrote:
> > [External Email]
> >
> > Dear all,
> >
> > So I am doing some work related to my thesis and would like to
> acknowledge whether I am doing is correct and later on proceed with the MD
> sim, I am working with 3POV as the PDB file, and I fixed the missing chains
> or residues which is normal using chimerax ( modeler ) , and then I used
> pdb fixer to make sure everything is fixed and then its converted using
> pdb4amber, after this I had used reduce in the command line, and then
> preceded to tleap.
> >
> > However , when I had used I get warnings when its loaded into tleap ,
> so is this fine ? , and I know that I will get to energy minimization prior
> to the actual simulation itself.
> >
> > Best,
> > Abdulrahman
> >
> >
> >
> > Abdulrahman Walid Attia Ibrahim ElBagoury
> > Antivirale und Antivirulenz-Wirkstoffe
> >
> > Helmholtz-Institut für Pharmazeutische Forschung Saarland
> >
> > University Campus E8.1, 66123 Saarbrücken
> >
> >
> >
> [cid:Helmholtz_Submarke_HIPS_DE_RGB_ab888326-d1f3-4691-8fd5-14b7f77ded78.jpg]<
> https://www.helmholtz-hips.de/de/>
> >
> > Ein Standort des Helmholtz-Zentrums für Infektionsforschung GmbH (HZI),
> Braunschweig, in Kooperation
> > mit der Universität des Saarlandes
> >
> >
> >
> >
> > ________________________________
> >
> > Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 |
> 38124 Braunschweig | http://www.helmholtz-hzi.de/
> >
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> für Wissenschaft und Kultur
> > Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger -
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> >
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> --
> Dr. Adrian E. Roitberg
> Frank E. Harris Professor
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
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Received on Fri Apr 24 2026 - 10:30:02 PDT
