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
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Received on Thu Feb 10 2022 - 11:00:02 PST
