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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 12 2021 - 05:00:03 PDT
