[gmx-users] drug topology file

Justin Lemkul jalemkul at vt.edu
Wed Jan 30 21:43:29 CET 2013

On 1/30/13 3:27 PM, az kalsom wrote:
> hi,
>   i wanted to know, what s simple way to correct the topology generated by
> PROGRG server
> i have read the paper mentioned in tutorial , but still i am nt able to
> correct the file
> please help me, should all CH3 CH2 charge ne made zero ?

Not necessarily.  Deriving parameters for the Gromos96 force fields is a 
somewhat ill-defined process, as iterative empirical refinements are often used. 
  Building blocks of common functional groups are generally transferable between 
molecules, and recent papers have suggested parameters for many non-protein 
groups.  There are probably a dozen or so papers that I would consider necessary 
reading before you should attempt to parameterize any molecule under Gromos96.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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