To whom it may concern,
Hello, I am learning Amber for the first time, and I would really
appreciate any advice/tips you can offer.
I would like to build a box of 1-octanol molecules and use the GAFF force
field to perform MD simulations. I have gone through several of the
tutorials available online (enormously helpful, by the way) and had success
running MD on a single molecule of 1-octanol.
I have built pdb files for boxes of octanol molecules using other programs,
but I was unable to get Amber to read these files properly. Can Xleap, or
any of the other utilities within Amber, be used to build a pdb file
corresponding to a box of several (e.g., a few hundred) octanol molecules?
Thank you for your time.
Regards,
Marianna
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Received on Tue May 06 2014 - 23:30:02 PDT
