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?
>
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> -----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 Mon Jul 22 2019 - 14:00:03 PDT
