I am working on silver nanoparticle interaction with the signal peptides of the microbes. I would like to work on protein-Ligand docking studies, but I am unable to find the silver nanoparticle .pdb and other format files for docking purpose. I mean while I had used the silver ion .pdb file , I think the silver ion is not itself a nanoparticle, please provide suggestions in this regard
I think you will get the pdb files of peptides from Protein Data Bank but not silver nano-particles. First find out the structure of nano particles which you are going to take as ligand, then you can draw it using softwares like Chemdraw Ultra and copy it as smiles and those smiles can be converted to Pdb. files.
I am not 100% sure, but you can try.
Arushdeep Sidana, Thanks for your response, i had that problem how can i determine the structure of the Silver nanoparticle, i tried to build the complex structure of the silver by adjoining the atoms of the silver ions to each other by using Chem-draw.
But how can i finalise that it would be the structure of the silver nanoparticle, according to the present literature, i can find the structure of the nanoparticle will be square, quadrilaterals, triangles etc., but upto what extent the nanoparticle will contains that much of the silver and its capping agent, please suggest further
Hi, I also have this problem. Have you found any reasonable answer for drawing a silver nanoparticle?
hi, i am not able to get the pdb format of silver nanopartilces. if u have can u please help me
Hi Narayanaswamy Krithiga,
I agree with Andudeep Sidana
PDB itself is a protien data base. So you don't get a silver nano particle as a pdb because silver nanoparticle is not a protein. That becomes your ligand.
You can use the chembiodraw and create a mol. file. If the structure you designed is different from the pictures, don't worry. Do the energy minimization of the ligand and then perform the docking. If the structure is same, then it is of no problem.
Regards
Harsha
You can sketch your own .pdb files using Material studio and VMD tool in two steps.
This question is too old, but I am responding to future students
you can request from anther in this filed .
please find attached
good luck
Topology file and coordinate and ....For gromacs
If you know the lattice constant for silver crystal then you easily can create the silver NP with suitable for you radius with Openmd package: http://openmd.org/building-and-equilibrating-a-gold-nanoparticle-in-openmd/
You can use Samson. Easy to operate and there's some in built nano-particle composite.
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