AMBER Archive (2007)

Subject: AMBER: gibbs problems

From: JAVIER PEREZ (javier.perez_at_uab.es)
Date: Wed Oct 31 2007 - 05:48:22 CST

Hi amber users,
 
I am working with FEP calculations using gibbs. When a FEP calculation
finishes, I obtain a .trj file, a .mst file, an .out file and a .rst file
which contains information about the final state of the perturbation. I
would like to use that restart file as a starting point for a Molecular
dynamic simulation. I think that I should use the perturbated topology file
created in xleap and used previously for FEP calculations.
 
My problem is that I do not know which flags I should add in my molecular
dynamics input file to run a simulation using the structure with
perturbation. I have carefully read the amber manual. However, it does not
clarify my doubts.
 
Any suggestion will be welcome.
 
 
Javier Perez
 
 
******************************
Javier Perez
 
Teaching assistant
 
Chemistry Department
Universitat Autonoma de Barcelona
08193 Bellaterra (Barcelona)
 
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