[gmx-users] nanoparticle-protein simulation

[jahanshah ashkani]

Hi there,
I would be glad if somebody let me know how I can simulate a Nanoparticle-protein complex by GROMACS.
Thank you very much.

Best,
J

Jahanshah Ashkani,

PhD student of Biotechnology & Genetics,

University of the Western Cape,

Biotechnology Department,

Private Bag X17,

7735 Bellville,

Cape Town,

South Africa

jashkani at mail.biotech.uwc.ac.za

--- On Thu, 10/23/08, Abu Naser <likhonnaser at hotmail.com> wrote:
From: Abu Naser <likhonnaser at hotmail.com>
Subject: RE: [gmx-users] spliting clusters.pdb
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Thursday, October 23, 2008, 5:08 AM




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Hi Jochen,

 

Thanks for your replay. I manage to do that using trjconv. However, I will keep your

suggestion in my mind for future use.









 

> Date: Wed, 22 Oct 2008 18:04:01 +0200
> From: jhub at gwdg.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] spliting clusters.pdb
> 
> Abu Naser wrote:
> > Hi All,
> > 
> > I have been wondering whether there is any tools for spliting clusters.pdb file into individual snapshots.
> 
> If there is a TER between the structures, the shell command csplit may
> be useful for you.
> 
> Jochen
> 
> 
> > 
> > With regards,
> > 
> > Abu
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > _________________________________________________________________
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> > 
> > 
> > ------------------------------------------------------------------------
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> 
> -- 
> ************************************************
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
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