AMBER: Is the MD simulation normal

From: Shulin Zhuang <>
Date: Thu, 26 May 2005 23:30:48 +0800

Dear everybody,

Now, I have a very troublesome problem. I have performed one MD
simulation on a protein-inhibitor complex with its X-crystal structure
as the initial structure. In the X-crystal structure, the inhibitor
has two important hydrogen bonds with the protein. For each of two
hydrogen bonds, the distance between donor and receptor is within 3

I use ff03 force field to carry out the MD simulation with Amber8.
The partial atomic charge for the ligand was generated using RESP
 I use constraint minimization and constraint NVT MD of 50 ps to heat
up the solvated system.

After the minimization and NVT MD, I get the complex structures using
command ambpdb with the generated restrt file and find that after the
minimization stage or after the NVT MD stage, the two important
hydrogen bonds still exsit.

However, After 1 ns NPT MD, the two important hydrogen bonds were
lost. I roughly measure the -- the distance between donor and
receptor , the distance become 2 or 3 angstrom larger than the former

Is my NPT MD normal? If it is wrong, where is the problem.

Looking forward to the answer!

Best regards!
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Received on Thu May 26 2005 - 16:53:01 PDT
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