AMBER Archive (2009)

Subject: Re: [AMBER] I need a professional help about xleap and pdb file

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Fri Feb 27 2009 - 08:17:31 CST

Nancy
 
The problem is not with your pdb file. xleap lacks the proper force
field parameters. You may be able to generate a reasonable set with
antechamber/xred. Good luck.
 
Pete

>>> On 2/27/2009 at 8:56 AM, in message
<23004468.543221235742974826.JavaMail.coremail_at_bj163app78.163.com>,
nancy4619 <nancy4619_at_163.com> wrote:

Dear all , I have a problem when I load pdb file with order
nan=loadpdb nanotube.pdb. My pdb file is about carbon nanotubes ,They
are nanotube.pdb and nanotube.txt.The problem is in the Screenshot
-1.png ,my software is amber10,I don't know what is wrong with my pdb
file and how to modify it,can any boby help me?
Looking forwarding to your reply soon! Thanks a lot! Enjoy a good
weekend!
                                             Nancy

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