AMBER Archive (2006)

Subject: AMBER: different TI calculations starting from the same state

From: Andrea Bortolato (andrea.bortolato.1_at_unipd.it)
Date: Fri May 26 2006 - 05:12:12 CDT

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
information.

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

---------------------------------------
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
e-mail:andrea.bortolato.1_at_unipd.it
Webpage URL http://mms.dsfarm.unipd.it
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