Re: [AMBER] system preparation error

From: David A Case <>
Date: Thu, 12 Aug 2021 07:19:10 -0400

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

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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Received on Thu Aug 12 2021 - 04:30:02 PDT
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