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
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Received on Thu Feb 01 2018 - 02:30:02 PST
