From: Babban Mia (babbanmia_at_gmail.com)
Date: Wed Aug 10 2011 - 22:58:19 CDT
As I had mentioned in my last post that I am setting up a solvation box
having ethanol and water molecules which I created using packmol.
To be able to use the pdb file of that simulation file which has water in
TIP3 representation ,ethanol molecules and protein ,I need a single topology
file which would find representation for all things present in the
I am currently using top all27_lipid topology file which has representation
for my entire protein and water molecules in TIP3 represenation
*Can somebody please advise me about a topology file which would cater to my
ethanol molecules as well ?
Is the TIP3 representation good enough when water is being used as solvent
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