Re: AMBER: lib file for nonstandard residue

From: David A. Case <>
Date: Thu, 14 Jul 2005 15:35:47 -0700

On Thu, Jul 14, 2005, Eric Hu wrote:

> So what does childsequence mean? I have seen a much larger number
> (>5000) here for other proteins such as the one in Ross Walker's
> non-standard residue tutorial. Also the simulation seems to work fine
> and DIK would have crazy move if both ends are not connected to the
> protein.

It is certainly advisable to use rdparm to check what bonds are actually
in your prmtop file, to make sure that the connectivity is what you want.
I don't know how you made your pdb file (the one with the TER after DIK);
if you haven't already done so, try ambpdb and see what it gives.


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Received on Thu Jul 14 2005 - 23:53:00 PDT
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