I can't fault anything but I'm not the most expert here.
However, like I said before, replace
addions solvcomplex Cl- 0
addions solvcomplex Na+ 0
with addIonsRand (you need to read about this command). Read about addions
as well to understand how it works.
You definitely don't want that ion inside the pocket.
On Thu, 10 Feb 2022 at 18:36, Renato Araujo <renatoacufpa.gmail.com> wrote:
> How did you get the topology and parameters for your ligand? How were the
> partial charges calculated? Are there, in the protein pocket, residues that
> may have different protonations like HIS?
>
> Partial charges were calculated by gaussian09.
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt # iop(6/5
> 0=1).
>
> Then
>
> antechamber -fi gout -fo ac -nc 0 -i lig.log -o input.ac -c resp
> antechamber -fi ac -i input.ac -c wc -cf input.crg
> antechamber -fi pdb -fo mol2 -i lig.pdb -o lig.mol2 -c rc -cf input.crg -j
> 4 -at gaff2
> parmchk2 -i lig.mol2 -f mol2 -o lig.frcmod.
>
> Afterwards I used tleap to generate my files.
>
> source leaprc.protein.ff14SB
> source leaprc.gaff2
> source leaprc.water.tip3p
> loadamberparams frcmod.ionsjc_tip3p
> set default PBRadii mbondi2
> rec=loadpdb pro.pdb
> loadamberparams lig.frcmod
> LIG=loadmol2 lig.mol2
> gascomplex= combine {rec LIG}
> savepdb gascomplex complex.pdb
> saveamberparm gascomplex complex.parm7 complex.rst7
> saveamberparm rec receptor.parm7 receptor.rst7
> saveamberparm LIG ligand.parm7 ligand.rst7
> solvcomplex= combine {rec LIG}
> solvateoct solvcomplex TIP3PBOX 12.0
> addions solvcomplex Cl- 0
> addions solvcomplex Na+ 0
> savepdb solvcomplex complex_solv.pdb
> charge solvcomplex
> check solvcomplex
> saveamberparm solvcomplex complex_solv.parm7 complex_solv.rst7
> quit
>
> these were the steps.
>
> Who adds the Na+ ions is the tleap
>
> Em qui., 10 de fev. de 2022 às 15:19, Alan <alanwilter.gmail.com>
> escreveu:
>
> > How did you get the topology and parameters for your ligand? How were the
> > partial charges calculated? Are there, in the protein pocket, residues
> that
> > may have different protonations like HIS?
> >
> > You shouldn't have NA+ inside the enzyme pocket. Try addIonsRand instead
> > of addIons in tleap.
> >
> > On Thu, 10 Feb 2022 at 13:52, Renato Araujo <renatoacufpa.gmail.com>
> > wrote:
> >
> > > Dear amber users
> > >
> > > I'm facing a problem in a protein-binding simulation
> > >
> > > I'm trying to simulate 100ns of molecular dynamics.
> > >
> > > I made the coupling and later the Dynamic process
> > >
> > > 1) In the initial 40ns, my ligand moves away from the binding site and
> > > consequently from the enzyme.
> > >
> > > What can I do to solve this problem?
> > >
> > > 2) When preparing the system in tleap, I notice that a Na+ is placed
> very
> > > close to my ligand and remains there during the entire simulation time,
> > is
> > > this a problem? if yes how to solve?
> > >
> > > follow the image
> > >
> > > thanks
> > >
> > > --
> > > Prof Dr Renato Costa
> > > Instituto Federal do Pará - IFPA
> > > Grupo de Modelagem Molecular - UFPA
> > > Tel.+55 91 985484622
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Alan Silva 🚲🏊♂🏃♂🇧🇷🇫🇷🇬🇧
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Silva 🚲🏊♂🏃♂🇧🇷🇫🇷🇬🇧
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Received on Thu Feb 10 2022 - 11:30:02 PST
