Re: Nano-bio interaction in NAMD

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Oct 24 2018 - 16:23:33 CDT

A Google search should have revealed the aptly titled paper "On Atomistic
and Coarse-Grained Models for C60 Fullerene" by Luca Monticelli (
https://doi.org/10.1021/ct3000102 ).

You can produce parameters consistent with the CHARMM General Force Field
using: https://cgenff.umaryland.edu/
It gives the warning "typer WARNING: fullerene-like structure not
explicitly supported"; however, I'm not convinced that the parameters are
any worse than your other options.

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us

On Tue, Oct 23, 2018 at 10:03 AM Ashkan Shekaari <shekaari_at_email.kntu.ac.ir>
wrote:

> *Dear experts,*
>
> *Is it possible simulating the interaction of a nanostructure (such as
> fullerene) with a biological matter like a protein using NAMD?*
> *If so, is there any force field file to describe such a nano-bio
> interaction?*
>
> *--*
> *With my best regards,*
> *Ashkan Shekaari,*
> *Ph.D Candidate in Solid State Physics,*
> *K. N. Toosi University of Technology,*
> *Tehran, Iran*
>
> --
> This message has been scanned for viruses and dangerous content by
> *KNTU Antispam System (E.F.A. Project)*
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.efa-2Dproject.org&d=DwMCaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=b9C8OXptmIe7ysVrNcfRSedXnr6C-whPDtxLxE73phw&s=CA_y_zZwgt8G5TFXqkRZK9dT6otOcbn1jMsI5JK4MEY&e=>,
> and is believed to be clean.
>

This archive was generated by hypermail 2.1.6 : Wed Sep 18 2019 - 23:20:23 CDT