AMBER Archive (2007)

Subject: AMBER: problem regarding water handling in explicit simu

From: gurpreet singh (gps.iitm_at_gmail.com)
Date: Fri Mar 30 2007 - 03:35:49 CST

hello Amber users

i musing Amber 9 for carrying an explicit simulation i want to ask two
questions:

1) i want to remove a particular water molecule from my ongoing simulation ,
how can i make the corresponding topology file ie topology file with that
water removed, and how can i get the corresponding restart file with all the
velocity information intact but with removal of information related to that
particulat water molecule
i can use ptraj strip command but that usually dont give the velocity
information in the output file we got from it

2) if i want to restrict the water molecules to reach a particular area in
the protein then is their any way in amber by which i can create this type
of potential barrier so that water or any solvent molecule dont come near
that place

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