AMBER Archive (2009)

Subject: Re:Re: [AMBER] A problem with xleap and pdb file

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Fri Feb 27 2009 - 08:32:20 CST

You might try changing the atom type to CA (sp2 aromatic carbon). Others have argued that a nanotube carbon is fairly rigid and comprised of just aromatic like carbons (Rink, et.al. Chem Phys 327 98-104 (2006) and others). But how you approach this depends on what you want to know and how important it is to have good force field parameters.
 
Pete

>>> On 2/27/2009 at 9:20 AM, in message <20622778.549641235744417408.JavaMail.coremail_at_bj163app78.163.com>, nancy4619 <nancy4619_at_163.com> wrote:

I have renamed C atoms C1 ,C2... but I can't produce .top and .crd file too. I have searched on google "nanotubes Amber",but no useful answer ,if you can ,can you give me an explicit explanation?
                                             Nancy

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