Hi Nancy,
Setting up something like a carbon nanotube is not a trivial matter and you
really need to obtain an understanding of how amber functions, how the force
field parameters are generated and assigned etc. With this knowledge it then
becomes clear what needs to be done and why. I suggest you work through
Tutorial A1 on the amber website.
http://ambermd.org/tutorials/
This will give you an idea of how to setup non standard systems etc and
should ultimately help you in building a nanotube etc.
Good luck,
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of nancy4619
> Sent: Friday, February 27, 2009 6:20 AM
> To: AMBER Mailing List
> Subject: Re:Re: [AMBER] A problem with xleap and pdb file
>
>
> 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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Received on Sat Feb 28 2009 - 08:48:18 PST
