AMBER Archive (2003)

Subject: AMBER: water box problem

From: Omar Wahab (paxomw_at_nottingham.ac.uk)
Date: Thu Jul 24 2003 - 03:32:35 CDT

Dear AMBER users,

     I am trying to simulate the unfolding of an RNA duplex in explicit solvent. I want to keep the amount of waters in the system to a minimum. I want to make a box with dimensions of approximately 40Ax40Ax100A with the solute positioned close to one end of the box rather than the centre of the box which Xleap produces. Is ther any way to position the solute at one end of the box as opposed to the centre?

     Thanks,
    Omar Wahab

   Omar Wahab
   PhD Student=20
   Computational Modelling and Informatics Group
   School of Pharmaceutical Sciences
   University of Nottingham
   Nottingham NG7 2RD

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