Re: [AMBER] Question on the construction of a topology file

From: Daniel Roe <>
Date: Tue, 28 Jun 2011 00:57:37 -0400


When I use the same commands in leap I don't see the same behavior
(long bond to H). What version of AmberTools are you using?

That being said, as long as you are careful with your minimization the
bond to H should go back to where it should be. Definitely don't run
any MD until the bond is back to normal though.


On Fri, Jun 24, 2011 at 5:31 PM, <> wrote:
> Hello,
> I am somewhat inexperienced with Amber and I have a question on something I
> did.
> I am simulating Alanine Dipeptide and I constructed the topology file using
> tleap in Amber10 using the following set of commands:
> A = sequence {ACE ALA NME}
> impose A {1 2 3} {{N CA C N -40.0} {C N CA C -60.0}}
> The resulting structure looks ok in VMD, but it has one hydrogen atom which
> is very far away from the structure, causing an enormously long bond between
> it and the corresponding carbon atom.
> Should I be concerned about this or is it expected that in subsequent
> equilibrations it will resolve itself?
> Thank you very much in advance.
> _______________________________________________
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Received on Mon Jun 27 2011 - 22:00:04 PDT
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