Re: [AMBER] simulation runs very slow..

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Mon, 12 Jul 2010 08:41:43 -0700

> 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 ...
> 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?

The best approach would be to add CONECT records to the pdb by
modifying the code in ambpdb. Then the visualiser would know
the bond is there.

Short of that, the only way I can think of to tell if the bond is
there is by running dynamics and making sure the distance is reasonable.


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Received on Mon Jul 12 2010 - 09:00:03 PDT
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