AMBER: Implicit 4r md

From: yen li <>
Date: Tue, 30 Nov 2004 08:58:34 -0800 (PST)

hello amber,
I am performing Implicit solvent md on small proteins using 4r dielectric, restraing the helices ans sheets. The input file for the initial minimization step is:
        maxcyc=1000, ncyc=500,
restraint 1
RES 10 19
RES 25 37
RES 42 55
My problem is that the total energy at the start of the minimization is positive and after the minimization (1000 steps) is positive. Is there someting which i am doing wrong, because of which total energy is positive. I am attaching the output file.

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Received on Tue Nov 30 2004 - 17:53:00 PST
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