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 - 06:30:02 PDT
