VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Feb 13 2018 - 09:38:45 CST

Both programs I linked (EMC or Moltemplate) are designed to generate
initial coordinates. Read the documentation to see how to wrap the polymer.

Giacomo

On Tue, Feb 13, 2018 at 2:38 AM, soroush ziaei <soroush.ziaei7337_at_gmail.com>
wrote:

> thanks dr.fiorin,
> i know VMD supports model building with the CHARMM force field natively
> but i want to know which program can wrapping a polymer around the CNT ?
>
> best regard,
> soroush
>
> On Fri, Feb 2, 2018 at 7:21 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi Soroush, VMD supports model building with the CHARMM force field
>> natively. If you're using CHARMM (note: that is entirely *your* choice:
>> there are many others) you only need to find force field files with support
>> for PEG chains, or build them yourself. Searching the literature or the
>> CHARMM forum may be a good start.
>>
>> Once you have force field files, VMD has a couple of tools that can help
>> build and manipulate the system topology (PSF file):
>> http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/
>> http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/
>>
>> As for generating an initial set of coordinates (PDB file), a couple of
>> independent tools may be of help:
>> http://www.moltemplate.org/
>> http://montecarlo.sourceforge.net/emc/Welcome.html
>>
>> As for the number of polymer chains, you have to decide.
>>
>> Giacomo
>>
>> On Fri, Feb 2, 2018 at 8:21 AM, soroush ziaei <
>> soroush.ziaei7337_at_gmail.com> wrote:
>>
>>> hi there,
>>> i'm a researcher & i want to simulate some polymer such as PEG on CNT;
>>> how can i adding this polymer to the surface of CNT, wrapping or adding
>>> to the edge of CNT ?
>>> if wrapping around the CNT is the best item please tell me how to
>>> wrapping this polymer;
>>> by the way how many monomers needed? and how to repeating this monomer
>>> to build the polymer?
>>> if there is a site that can generate polymers in pdb,... format, tell me.
>>> thanks a million.
>>>
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin