Topology for CNT

User discussions
1

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,
Best

2

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.

3

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.

4

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.