Hi Renato,
On top of checking the commands Dave mentions, your problems seems to just
be an overflow of the pdb format. Check the end of the pdb file and you
might notice a shift of the columns, that causes this issue. The topology
and coordinate file might still be ok though, so try to open those in vmd
to check your system instead of the pdb file.
Cheers,
El jue, 12 ago 2021 a las 13:20, David A Case (<dacase.chem.rutgers.edu>)
escribió:
> 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
>
>
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>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Thu Aug 12 2021 - 05:00:02 PDT
