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
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Javier Perez
Teaching assistant
Chemistry Department
Universitat Autonoma de Barcelona
08193 Bellaterra (Barcelona)
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Received on Sun Nov 04 2007 - 06:07:07 PST
