AMBER: different TI calculations starting from the same state

From: Andrea Bortolato <>
Date: Fri, 26 May 2006 12:12:12 +0200

Dear all,

I have a protein-inhibitor complex, I created a
lib file with leap. I already did the
equilibration of the system.

Now I'd like to do several different TI
calculations changing different atoms starting
always from this state. I need to change the
topology file including the perturbation

I import the lib file in leap, I do the
change and I recreate the prmtop file with the
perturbation information. This new prmtop will be
compatible with the restrt coordinates (with the
velocity information) file of the equilibration?

Thank you,

Andrea Bortolato, Ph.D. Student

Molecular Modeling Section
Department of Pharmaceutical Sciences
University of Padova,
Via Marzolo, 5
35131 Padova - ITALY
Phone: +39-049-8275801
Fax: +39-049-8275366 or +39-049-8275704
Webpage URL
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Received on Fri May 26 2006 - 21:05:25 PDT
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