AMBER: the restraint MD fail with amber8,but success with amber7

From: Shulin Zhuang <>
Date: Fri, 13 May 2005 09:44:04 +0800


I have met with a strange problem.

When I perform the constant volume MD of a protein-ligand complex to
raise the temperatur from 0k to 300K, the temperature raise so quikly
that after 12 ps, it reach 300K. I have examined the one snapshot from
the constant volume MD and find the ligand conformation is much
differenct from the crystal and two hydrogen bonds lost.

Therefore I have to do the restraint MD to control the temperature.

The prmtop file and inpcrd file are made with amber8 using ff03.

When I use amber8 to perform the restraint MD, it fails and give the
following error:

     rfree: Error decoding variable 2 2 from:
Restrain the
     this indicates that your input contains
 incorrect information

But I use the same input file to perform restraint MD with amber7, it
is successful and no error occurs.

But I examine the amber7 output and find that, the temperature are not
under control.

What is the problem? How should I tackle it?

I set the temperature control that:


The time step is 0.002 ps.

According to the temperature control, the temperature should under 150
K before 15 ps(etc. 7500 steps), however, after 10.4 ps, the
temperature exceed 150 K.
At 15 ps, the temp is 296.7 K, after this the temp decrease, and at
20 ps the temp is 194.39 K. After 20 ps, the temp raise slowly.

Does the tempearature change normally?

The partial output file and input file are attached.

Thanks a lot!

Best regards

   Shulin Zhuang
Chemistry Department 
Zhejiang University PRC

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

Received on Fri May 13 2005 - 02:53:00 PDT
Custom Search