AMBER Archive (2008)

Subject: RE: AMBER: Disturb you for help!

From: Yong Duan (
Date: Mon Jan 14 2008 - 14:06:11 CST

As to your first question, you need to make sure that there is a bond in the
topology file. Displaying the molecule from xLeap should allow you to
inspect it. VMD can also do this is you use parm/parm7 in combination with
AMBER crd or AMBER restrt files. If indeed, there are bonds and the bond
forces are reasonable (on the order of 100 kcal/mol/A^2), we need to take a
look at your simulation conditions (temperature, etc.). Breaking bonds is
not easy in MD, actually, almost impossible with the present formula. If you
observe a broken bond, it is likely that there is no bond in your topology
file, meaning, your topology file is not the one that you intended to use.
As to your second question, this depends on your system. Many have used
energy as the sole criterion, while others have argued the need to include
entropic terms. In many cases, the lowest energy conformation can be close
to the average conformation of the lowest free energy state. There are also
plenty of occasions that the difference is substantial. Thoeretically, if
you intend to model the system at biologically-relevant environment (room
T), you need to consider free energy. Therefore, it is up to you and your
advisor to make the judgement as to whether the results are scientifically
-----Original Message-----
From: [] On Behalf Of
Sent: Monday, January 14, 2008 8:17 AM
Subject: AMBER: Disturb you for help!

Dear anyone who may concern this letter,
I came across two problems: one of the problem is that : when that I carry
out md simulation, I find the the two bonds of my ligand molecular become
disconnected; another problem is that when the md simulation is finished, I
can get a frame with the lowest energy. Can I say this frame is the best
conformation of my model, or it most like the crystal structure of the
Thanks in advance!
Best wishes
Rilei Yu



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