Topology for CNT

Dear all,

I am working on simulation of ssDna and CNT.
In this regard, I am using amber forcefield.

What is the best server for generating CNT topology as ligand?
And, is it possible to do CNT and ssDNA docking by AutoDock?

Many thanks in advance,

I wouldn’t use a server, I’d use gmx x2top, which is designed for this purpose.

Maybe, but this isn’t the best forum for such questions.

If you intend to you a server for CNT structure, CHARMM-GUI has a nanomaterial modeller. The problem is it could only generate pristine single walled CNTs.

As regards, ssDNA docking on CNTs, I have found that AutoDock Vina can be misleading. I have used several proteins (cytoplasmic enzymes and membrane proteins) for docking with CNTs but the results have been misleading. My suggestion is to look for any other alternatives. I haven’t worked with DNA per se but expect such misleading results to occur in DNA-CNT systems as well.

Hi rpsingh,
Thanks for your response.

How about .itp file?
Could you please tell me where I can generate an itp file for CNTs with corrected charges?

As far as I know atom charges in CNTs are mistaken upon generating itp files.

Thanks in advance for your help.