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
--
Regards
Garima Singh
AcSIR-PhD Fellow
Biotechnology Division
C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division)
Central Institute Of Medicinal And Aromatic Plant
CSIR-CIMAP
Lucknow
garimabioinfo.gmail.com
INDIA
Please don't print this e-mail unless you really need to. Be Green !
*Thank You and Best Wishes*
--
*Regards*
Garima Singh
AcSIR-PhD Fellow
Biotechnology Division
C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division)
Central Institute Of Medicinal And Aromatic Plant
CSIR-CIMAP
Lucknow
garimabioinfo.gmail.com
*INDIA* Please don't print this e-mail unless you really need to. Be Green !
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Received on Thu Feb 01 2018 - 02:30:02 PST
