Hi Garima,
There is a metal ion modeling tutorial for AMBER: http://ambermd.org/tutorials/advanced/tutorial20/index.htm <http://ambermd.org/tutorials/advanced/tutorial20/index.htm>.
You are going to use the 12-6 nonbonded model, right? If so, you can check the tutorial here: http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm <http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm>.
There are parameters for Pb2+ in the “frcmod.ions234lm_126_tip3p”, “frcmod.ions234lm_126_spce”, and “frcmod.ions234lm_126_tip4pew” files (which are the CM set, or called the normal usage set), I suggest you to check the section 3.6 in the AMBER 2017 manual: http://ambermd.org/doc12/Amber17.pdf <http://ambermd.org/doc12/Amber17.pdf>. There are also HFE parameter set for Pb2+ but I don’t think it is suitable for normal molecular dynamics production simulation.
Hope it helps,
Pengfei
> On Feb 1, 2018, at 4:19 AM, Lorenzo Gontrani <lorenzo.gontrani.uniroma1.it> wrote:
>
> You should insert any additional parameters into a frcmod file, that
> then you must tell tleap/xleap to source (loadamberparams myfile.frcmod).
>
> The nonbonded paramters should go in the NONBOND section, like this:
>
> NONBON
> P 2.1000 0.2000 same as p4
>
> Hope this helps!
>
> Lorenzo
>
>
>
> On 02/01/2018 11:03 AM, Garima Singh wrote:
>> Dear Amber user,
>>
>> I am trying MD calulation of my protein contains chelating Pb ion
>> in it . When I try to solvate the my Pb - protein complex using the
>> command *solvatebox mol TIP3PBOX 10 it gives **(using default radius
>> 1.500000 for PB)*
>> * (using default radius 1.500000 for PB)*
>> * (using default radius 1.500000 for PB)*
>> * Solute vdw bounding box: 35.813 33.915 30.346*
>> * Total bounding box for atom centers: 55.813 53.915 50.346*
>> * Solvent unit box: 18.774 18.774 18.774*
>> * (using default radius 1.500000 for PB)*
>> * (using default radius 1.500000 for PB)*
>> * (using default radius 1.500000 for PB)*
>> * Total vdw box size: 58.950 57.081 53.455 angstroms.*
>> * Volume: 179871.770 A^3 *
>> * Mass > 82480.242 amu, Density > 0.761 g/cc*
>> * (type - hence mass - of one or more atoms could not be found)*
>> * Added 4129 residues.*
>>
>> when I used the tLEAP procedure for *.prmtop and .inpcrd* files preparation
>> for my protein-metal complex following error occur
>>
>> *saveamberparm mol pb_pm.prmtop pb_pm.inpcrd*
>> Checking Unit.
>> WARNING: The unperturbed charge of the unit: 5.000000 is not zero.
>>
>> -- ignoring the warning.
>>
>> Building topology.
>> Building atom parameters.
>> For atom: .R<PB 82>.A<PB 1> Could not find vdW (or other) parameters for
>> type: Pb+
>> For atom: .R<PB 83>.A<PB 1> Could not find vdW (or other) parameters for
>> type: Pb+
>> For atom: .R<PB 84>.A<PB 1> Could not find vdW (or other) parameters for
>> type: Pb+
>> Parameter file was not saved.
>>
>>
>> This implies to me that it hasn't recognized the VDW radii for Pb++ ion
>> What command line should be added to tLEAP to account for vdW radii for
>> chelating Pb++ to solve the problem?
>>
>>
>>
>>
>>
>> Thank You and Best Wishes
>
> --
> ==========================================
> Lorenzo Gontrani
> Research associate - EDXD group
> University of Rome "La Sapienza"
> ResearcherID: L-6061-2014
> Scopus Author ID: 6506613970
> OrcID:0000-0001-8212-7029
>
> GSM +39 338 7615798
> Email lorenzo DOT gontrani AT uniroma1 DOT it
> Webpage: http://webcaminiti/gontrani.html <http://webcaminiti/gontrani.html>
> =========================================
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Received on Thu Feb 01 2018 - 08:30:03 PST
