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
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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 - 09:00:03 PDT
