AMBER Archive (2008)

Subject: Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating

From: David A. Case (
Date: Tue Jun 10 2008 - 07:50:27 CDT

On Tue, Jun 10, 2008, xiaonan zhang wrote:

> Then I start minimization, everything is OK. But when I just start heating
> process and visulized the trajectory with VMD. I found something very
> strange. i.e., The two N terminal nitrogens were far away from the original
> place and caused incredibly long N-H and N-C bonds.

> The temperature rise to 8.87 in just 10 steps!!!

This is normal: langevin thermostats reach the target temperature very

> BOND = 456.6235 ANGLE = 1821.7021 DIHED =

You do not have a large bond energy.

1. You may have an imaging problem: that the structure is OK, the nitrogens
involved are appearing to VMD in the wrong unit cell. This is not supposed
to happen, but you should check anyway. Use the image command in ptraj to
put all atoms back in the first unit cell, then visualize the molecule again.

2. You may be missing bonds to the N terminal nitrogens. Use the "desc"
command in LEaP to examine the atoms in the first residue of each chain, to
see what the nitrogens are bonded to. If some bonds are missing, then of
course the atoms will fly away.

...good luck...dac

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