AMBER Archive (2004)

Subject: AMBER: program compatibility

From: hj zou (
Date: Sun May 30 2004 - 21:07:39 CDT

Dear amber usersúČ
        I run into a problem on program compatibility.
    I have run molecular dynamics simulation of a system by using program GROMACS and many analysises are performed.As a part of analysis,now I want to calculate the binding free energy of the system by using MMPB/SA in AMBER.What should I do?Maybe there are two ways:
   1.Take the crystal coordinate as the initial structure ,and then solvate,minimize ,heat and equilibrate the system in AMBER.Take 100 snapshots from equilibration and calculate the binding free energy by using MMPB/SA.
   2.Take 100 snapshots from equilibration trajectory of GROMACS simulation,minimize these structures in AMBER and then calculate the binding free energy by using MMPB/SA.
   Are they both reasonable? which one is better?It seems that METHOD 1 is better.But all the other analysis results are based on the trajectory structure of GROMACS simulation.So,in my opinion,METHOD 2 is better.However, I am not sure whether it is reasonable or not as the 100 snapshots are taken from trajectory produced by another program.
   Are there any other better ways to solve this problem?
   Any suggestions are highly appreciated.
   Best regards,


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