[phenixbb] geometry minimization with ligand present

[CPMAS Chen]

This is great, thank you so much!

Since my structure is from NMR, it contains all protons.

Thanks!

Charles

On Thu, Oct 20, 2022 at 7:26 PM Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Charles,
>
> it should be as simple as
>
> phenix.geometry_minimization model.pdb ligand.cif
>
> However, note that geometry restraints used in this case are very
> simplistic, for example, there are no attraction term. This means
> helices may unfold unless you do a good thorough job defining secondary
> structure restraints (and generally restrain all known hydrogen bonds).
> You can do this by making a hydrogen bond restraint file:
>
> phenix.hbond model.pdb
>
> (model.pdb needs to have explicit H added)
>
> and then supply that file to the above minimization command:
>
> phenix.geometry_minimization model.pdb ligand.cif hbond.eff
>
> It may be a good idea to verify hbond.eff to make sure it is as complete
> and accurate as possible. This is because H-bond definitions in this
> file are made based on input model and if input model geometry isn't
> great, the H-bond annotations (and corresponding restraints) may not be
> accurate either.
>
> In summary, here are the steps:
>
> 1) Add H to the model:
>
> phenix.ready_set model.pdb
>
> 2) Make H-bond restraints definitions:
>
> phenix.hbond model_with_H.pdb
>
> This command will create hbonds_pymol.pml file that you can load into
> PyMol and see all H bonds as dashed line. This lets you verify all H
> bonds that the program found (or missed). Edit hbond.eff if needed.
>
> 3) Finally, run geometry regularization:
>
> phenix.geometry_minimization model.pdb ligand.cif hbond.eff
>
> Let me know if you have any questions! Good luck,
>
> Pavel
>
> On 10/19/22 19:04, CPMAS Chen wrote:
> > Hi, All,
> >
> > I have a structure calculated with NMR restraints but it has quite
> > some geometry violation, such as torsion angles, clashes etc.
> > The structure has a small molecule ligand bound.
> >
> > Is it possible to add an CIF file for the ligand and use
> > phenix.geometry_minimization to idealize/optimize the protein structure?
> >
> > I have tried the following and phenix reported an error for missing
> > CIF file.
> >
> > phenix.geometry_minimization model.pdb
> > pdb_intepretation.apply_cif_restraints.restraints_file_name=ligand.cif
> >
> > what would be the correct syntax to add ligand cif for this
> > geometry_minimization?
> >
> > Or what would be the proper way to idealize/optimize a protein
> > structure with ligands present?
> >
> > The structure optimization during NMR calculation is not good enough
> > in my case.
> >
> > Thanks!
> >
> > Charles
>


-- 

***************************************************

Charles Chen

Research Instructor

University of Pittsburgh School of Medicine

Department of Anesthesiology

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