[gmx-users] creating topology for ligand

neelam wafa neelam.wafa at gmail.com
Thu Mar 1 14:03:35 CET 2018

Dear gmx users

I am trying to run a protein ligand simmulation. How can i create topolgy
for ligand. prodrg topology is not reliable then which server or software
can be used?  can topology be created by T LEEP off ambertools package for
secondly how to select the boxtype as I am new to simmulation so cant fix
the problem.  Please also guide me what factors should be considered to
select the water model??
Thanks in advance.

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