Can you also explain which file you loaded into Vmd? I would recommend
against the pdb format for reasons explained earlier in this thread. Load
the prmtop and restart instead.
As a side note, I don't see any glycan force field in your inputs. For an
example of building and simulating the spike in Amber (including pdb files
in the supporting info), see my lab's recent JACS article on spike
simulations:
Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations
Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric
Pocket
Lucy Fallon, Kellon A. A. Belfon, Lauren Raguette, Yuzhang Wang, Darya
Stepanenko, Abbigayle Cuomo, Jose Guerra, Stephanie Budhan, Sarah Varghese,
Christopher P. Corbo, Robert C. Rizzo, and Carlos Simmerling*
J. Am. Chem. Soc. 2021, 143, 30, 11349–11360
Publication Date:July 16, 2021
https://doi.org/10.1021/jacs.1c00556
On Thu, Aug 12, 2021, 6:56 AM Renato Araujo <renatoacufpa.gmail.com> wrote:
> dear David The command I used was this:
>
> source leaprc.protein.ff14SB
> source leaprc.gaff2
> source leaprc.water.tip3p
> loadamberparams frcmod.ionsjc_tip3p
> set default PBRadii mbondi2
> loadamberparams lig_resp.frcmod
> loadoff LIG.lib
> rec = loadpdb pro.pdb
> LIG = loadmol2 lig_resp.mol2
> com = combine {rec LIG}
> savepdb LIG ligand.pdb
> saveamberparm LIG ligand.prmtop ligand.inpcrd
> savepdb rec receptor.pdb
> saveamberparm rec receptor.prmtop receptor.inpcrd
> savepdb com complex.pdb
> saveamberparm com complex.prmtop complex.inpcrd
> charge com
> addions com Na+ 0
> addions com Cl- 0
> charge com
> solvateOct com TIP3PBOX 12.0
> savepdb com complex_solv.pdb
> saveamberparm com complex_solv.prmtop complex_solv.inpcrd
> quit
>
>
>
> Em qui., 12 de ago. de 2021 às 08:19, David A Case <
> dacase.chem.rutgers.edu>
> escreveu:
>
> > On Thu, Aug 12, 2021, Renato Araujo wrote:
> > >
> > >I'm trying to run a molecular diamic simulation with the SARS-CoV-2
> Spike
> > >Protein protein.
> > >
> > >In preparing my system I'm using:
> > >
> > >source leaprc.protein.ff14SB
> > >source leaprc.gaff2
> > >source leaprc.water.tip3p
> > >loadamberparams frcmod.ionsjc_tip3p
> > >set default PBRadii mbondi2
> > >loadamberparams lig_resp.frcmod
> > >loadoff ON.lib
> > >rec = loadpdb pro.pdb
> > >LIG = loadmol2 lig_resp.mol2
> > >com = combine {rec ON}
> > >savepdb ON binding.pdb
> > >saveamberparm ON ligand.prmtop ligand.inpcrd
> > >savepdb rec receiver.pdb
> > >saveamberparm rec receiver.prmtop receiver.inpcrd
> > >savepdb with complex.pdb
> >
> > I'm confused here: this seems to be the first time that the unit "with"
> has
> > been referred to. Are you running this inside VMD?
> >
> > >saveamberparm with complex.prmtop complex.inpcrd
> > >cartoon with
> >
> > I don't recognize the tleap command "cartoon". Is this a VMD command?
> >
> > >additions with Na+ 0
> >
> > "additions" is also not a command I recognize; do you mean "addIons"?
> >
> > >additions with Cl- 0
> > >cartoon with
> > >solvateoct with TIP3PBOX 20.0
> > >savepdb with complex_solv.pdb
> > >saveamberparm with complex_solv.prmtop complex_solv.inpcrd
> > >quit
> > >
> >
> > Try to do a much simpler setup: use loadPdb to get some starting pdb (say
> > "pro.pdb") into tleap. The run solvateOct and savePdb. Look at that
> > structure. If that works, you can start to add complications to get to
> > what
> > you really want.
> >
> > The particular odd water structure you have rings vague bells, but I
> > can't remember why. Maybe someone else on the list will recognize it.
> >
> > ...good luck...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Prof Dr Renato Costa
> Instituto Federal do Pará - IFPA
> Grupo de Modelagem Molecular - UFPA
> Tel.+55 91 985484622
> _______________________________________________
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> AMBER.ambermd.org
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>
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Received on Thu Aug 12 2021 - 06:30:02 PDT
