[AMBER] Question on the construction of a topology file

From: <lnedialkova.gmail.com>
Date: Fri, 24 Jun 2011 17:31:24 -0400


I am somewhat inexperienced with Amber and I have a question on something I

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 Fri Jun 24 2011 - 15:00:03 PDT
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