Dear Nan Lin:
I am also doing MD for protein-ligand complex system, but for my system in the case ligand, amber says(error) couldn,t assign parameter for ligand. Could you provide me information how you would assign the parameter for the ligand.
thanks
siva
----- Original Message -----
From: Nan Lin
To: amber.scripps.edu
Sent: Monday, June 07, 2004 10:04 PM
Subject: AMBER: Constant Pressure Problem of MD
Hi,
I am running MD for a complex of protein + ligand with WAT under constant pressure. I can get a fairly equilibrated system after 500ps run. But the pressure value is not stable at all. It constantly changes in a range from -1000 to +1000, also the mean is around 0-1. I read some previous posts saying the pressure is not constant, but changes should only be in a range of a couple of hundreds. Anybody know what's the possible problem in my system?
Any suggestion is highly appreciated!
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Received on Tue Jun 08 2004 - 07:53:00 PDT
