[gmx-users] water in protein itp file

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 14 05:22:30 CET 2006

raja wrote:
> Dear Mark,
> Thanks for your immediate reply and good solution. But until before
> yours this mail, I was thinking that inclusion of water and restraining
> them with metal ion is a very common happening in MD. Since in my short
> spell of molecular modeling and drug design experience, I have found
> almost 75% of the drug targets are metalo-enzyme and if you can still
> probe its active site, can invariably find water ligating with metal in
> most of the cases (Say 90%). This water bound form is present until an
> external ligand or drug replace and ligate with metal ion for enzyme
> inhibition process. I am really wondering a case, which I think quite
> common, is not able to depict easily in gromacs. I am so interested to
> extend this topic, how other gromacs users depict this scenario in their
> simulation.... Am I doing any thing stupid, I doubt myself?

If you actually want accurate energetics, you should really be looking 
at QM-MM simulations, which are a whole different ballgame in complexity 
and cost. I understand GROMACS does interface with GAMESS for these 
kinds of simulations, but that's where my knowledge ends. You should 
definitely do some literature reading on QM-MM simulations and see what 
software people have actually been using successfully. Probably, you 
should use that, rather than trying to make GROMACS do the job.


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