Hello,
Check the proper syntax for 'bond' in leap. Your usage is not correct. The
proper usage is along the lines of "bond mol.1.CA mol.2.CA". Also, you
should visualize the prmtop and inpcrd directly in something like VMD, since
that program will definitely maintain the proper connectivity upon
visualization. Also keep your eyes open for any error messages that may pop
up when you use the "bond" command in leap. If you use it incorrectly, I'm
guessing you'll get an error message.
Good luck!
Jason
On Mon, Jul 12, 2010 at 11:18 AM, Catein Catherine
<askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
>
>
> I have defined a new bond between residues 1 and 2 by using the "bone CA.1CA.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,
>
>
>
> Catherine.
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jul 12 2010 - 08:30:11 PDT
