I have set with this variable name only
com=loadpdb complex_42_final_2_noH.pdb
charge com
Total unperturbed charge: -6.001000
Total perturbed charge: -6.001000
On Tue, Jul 23, 2019 at 6:51 PM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Dear shivangi agarwal,
>
> Please pay attention to the error message, it's very descriptive:
>
> *addions com Na+ 6*
> Error: addIons: Argument #2 is type String must be of type: [unit]
>
> Your second argument "com" is not a unit but a string, that's probably
> because you haven't set or load the unit with this variable name...
>
> Best,
>
> Matias
>
> ----- Mensaje original -----
> De: "shivangi agarwal" <shiviagarwalpharma.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Martes, 23 de Julio 2019 4:02:34
> Asunto: Re: [AMBER] Error in preparing system using AmberTools19
>
> As per above two suggestions, I have not loaded ions94.lib this time and
> loadamberparams frcmod.ionsjc_tip3p because they are taken care by source
> leaprc.water.tip3p, but then also I am getting error during addions
> command. Please look into below commands and suggest.
>
> *source leaprc.water.tip3p*
> ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p
> ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p done
> Loading library: ./atomic_ions.lib
> Loading library: /home/ravi/anaconda3/dat/leap/lib/solvents.lib
> Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> This is the additional/replacement parameter set for TIP3P water
> Loading parameters:
> /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6
> normal usage set)
> Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
> JPCB (2008)
> Loading parameters:
> /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_126_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water
> model (12-6 normal usage set)
> *solvateBox com TIP3PBOX 10.0*
> Solute vdw bounding box: 48.246 52.899 51.490
> Total bounding box for atom centers: 68.246 72.899 71.490
> Solvent unit box: 18.774 18.774 18.774
> Total vdw box size: 71.546 76.278 74.743 angstroms.
> Volume: 407905.669 A^3
> Total mass 198107.200 amu, Density 0.806 g/cc
> Added 9443 residues.
> *charge com*
> Total unperturbed charge: -6.001000
> Total perturbed charge: -6.001000
> *addions com Na+ 6*
> Error: addIons: Argument #2 is type String must be of type: [unit]
> addIons unit ion1 #ion1 [ion2 #ion2]
> UNIT _unit_
> UNIT _ion1_
> NUMBER _#ion1_
> UNIT _ion2_
> NUMBER _#ion2_
> Adds counterions in a shell around _unit_ using a Coulombic potential
> on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
> opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
> the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
> If solvent is present, it is ignored in the charge and steric calculations,
> and if an ion has a steric conflict with a solvent molecule, the ion is
> moved to the center of said molecule, and the latter is deleted. (To
> avoid this behavior, either solvate _after_ addIons, or use addIons2.)
> Ions must be monoatomic. Note that the one-at-a-time procedure is not
> guaranteed to globally minimize the electrostatic energy. When neutralizing
> regular-backbone nucleic acids, the first cations will generally be added
> between phosphates, leaving the final two ions to be placed somewhere
> around
> the middle of the molecule.
> The default grid resolution is 1 Angstrom, extending from an inner radius
> of (max ion size + max solute atom size) to an outer radius 4 Angstroms
> beyond. A distance-dependent dielectric is used for speed.
>
> On Tue, Jul 23, 2019 at 2:17 AM Matias Machado <mmachado.pasteur.edu.uy>
> wrote:
>
> > Dear shivangi agarwal,
> >
> > The error you are having is expected due to the ion library you are
> > loading...
> >
> > If you edit "ions94.lib" you will see that the atom type for residue
> "Na+"
> > is "IP", however the frcmod file you are loading uses a different
> > atom-type, which is named "Na+" (yes the same name as the residue)...
> >
> > Then the correct way to load the parameters (before anything else!) is by
> > the following command:
> >
> > source leaprc.water.tip3p
> >
> > Notice that this "cmd" file loads the compatible library
> "atomic_ions.lib"
> > and parameters "frcmod.ionsjc_tip3p" for the corresponding water model...
> >
> > I encourage you (and anybody) to use the provided cmd files by
> developers,
> > they made a big effort to grant an easy to use, consistent, compatible
> and
> > checked set of parameters.
> >
> > Best,
> >
> > Matias
> >
> > ------------------------------------
> > PhD.
> > Researcher at Biomolecular Simulations Lab.
> > Institut Pasteur de Montevideo | Uruguay
> > [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> > [http://www.sirahff.com]
> >
> > ----- Mensaje original -----
> > De: "shivangi agarwal" <shiviagarwalpharma.gmail.com>
> > Para: "jimkress 58" <jimkress_58.kressworks.org>, "AMBER Mailing List" <
> > amber.ambermd.org>
> > Enviados: Lunes, 22 de Julio 2019 15:00:51
> > Asunto: Re: [AMBER] Error in preparing system using AmberTools19
> >
> > Yes I have loaded
> > solvateBox com TIP3PBOX 10.0
> > loadoff ions94.lib
> > addions com Na+ 6
> > loadamberparams frcmod.ionsjc_tip3p
> > saveamberparm complex complex-box.prmtop complex-box.inpcrd
> > Then getting error as mentioned above..
> >
> > On Mon, Jul 22, 2019, 11:25 PM James Kress <jimkress_58.kressworks.org
> > wrote:
> >
> > > Did you load the solvent and did the solvent file contain ion
> parameters?
> > >
> > > James Kress Ph.D., President
> > > The KressWorksR Institute
> > > An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
> > > "ENGINEERING THE CURE" C
> > > (248) 573-5499
> > >
> > > Learn More and Donate At:
> > > Website: http://www.kressworks.org
> > > Facebook: https://www.facebook.com/KressWorks.Institute/
> > >
> > > -----Original Message-----
> > > From: shivangi agarwal <shiviagarwalpharma.gmail.com>
> > > Sent: Monday, July 22, 2019 12:30 PM
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Subject: [AMBER] Error in preparing system using AmberTools19
> > >
> > > Hello everyone
> > >
> > >
> > > I have newly installed AmberTools19 on my system.
> > > When I am preparing my system for equilibration, I am getting error
> > > messages
> > > when I am saving prmtop and inpcrd after neutralizing my system.
> > > In this case there was -6 charge, so I have added Na+ 6 to neutralize
> it.
> > > And when I am saving prmtop and inpcrd, i am getting error as:
> > > Error: For atom (.R<Na+ 9705>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP)
> > > Error: For atom (.R<Na+ 9706>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP)
> > > Error: For atom (.R<Na+ 9707>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP)
> > > Error: For atom (.R<Na+ 9708>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP)
> > > Error: For atom (.R<Na+ 9709>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP)
> > > Error: For atom (.R<Na+ 9710>.A<Na+ 1>) could not find vdW (or other)
> > > parameters for type (IP).
> > >
> > > Even, when I am adding Cl- to another system, getting same error for
> cl-.
> > > Can somebody suggest where the problem is?
> > > Is the AmberTools19 has not been correctly installed?
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Received on Tue Jul 23 2019 - 10:30:01 PDT
