Thanks Jason!
Your reply was really helpful!
Kind regards,
Nicolas Genin
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: 12 November 2014 16:34
To: AMBER Mailing List
Subject: Re: [AMBER] [Amber] Amber14 does not find parameters for Mg2+, please help
> On Nov 12, 2014, at 10:35 AM, Genin, Nicolas J <n.genin12.imperial.ac.uk> wrote:
>
> Hi all,
>
> I have a little issue in order to generate the right parameters for atom type Mg2+ with Amber14.
> Please see below the input file and commands.
>
>
> PDB file:
> ATOM 30471 MG MG A2001 -1.069 -2.616 46.237 1.00 96.20 MGMG
> ATOM 30472 MG MG A2002 -3.875 -3.619 47.929 1.00100.04 MGMG
> TER 30473 MG A2002
>
> After executing the following xleap commands:
> source leaprc.ff14SB
> sys = loadpdb mg.pdb
>
> and when executing the following xLeap command:
> saveamberparm sys mg.prmtop mg.inpcrd
>
> xLeap does not appear to find a non-bonded parameter in its internal libraries for atom type MG:
>
> “Checking Unit.
> WARNING: The unperturbed charge of the unit: -81.000000 is not zero.
> WARNING: The perturbed charge: -81.000000 is not zero.
>
> -- ignoring the warnings.
>
> Building topology.
> Building atom parameters.
> For atom: .R<MG 3760>.A<MG 1> Could not find vdW (or other) parameters for type: Mg2+
> For atom: .R<MG 3761>.A<MG 1> Could not find vdW (or other) parameters for type: Mg2+
> Parameter file was not saved. “
>
> Could someone help me with this issue?
You need to load the ion parameters for the water model you want to use.
Note there are more options for divalent metal ions like Mg, so you need to choose which set of parameters to choose (hydration free energy-optimized or coordination number-optimized) or if you want to use the new 12-6-4 Lennard Jones potential to get both of them.
The manual has a chapter on ions that has more information that can help here.
HTH,
Jason
>
>
> Kind regards,
>
> Nicolas Genin
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Nov 12 2014 - 11:30:02 PST
