Re: [AMBER] simulation runs very slow..

From: Catein Catherine <>
Date: Mon, 12 Jul 2010 23:18:02 +0800

Dear Sir/Madam,


I have defined a new bond between residues 1 and 2 by using the "bone CA.1 CA.2" in xleap when I prepare the prmtop and inpcrd files (the force field parameters are available in standard AMBER force field already, so no addtional parameters needed to be inputed.


However, when I open used the ambpdb comand to convert the prmtop/inpcrd, and open the pdb file with visualizing programs (such as accerly DS visualizer), the bond I defined is missing. Why is it? How can I reconfirm if the bond is indeed considered during the simulation?


Best regards,


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Received on Mon Jul 12 2010 - 08:30:10 PDT
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