[gmx-users] water in protein itp file

raja raja_28 at fastmail.us
Tue Nov 14 05:05:25 CET 2006

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?

Regards and thanks!

On Tue, 14 Nov 2006 14:49:27 +1100, "Mark Abraham"
<Mark.Abraham at anu.edu.au> said:
> raja wrote:
> > Dear gmxions,
> > I want to include one crystal water within protein itp, to further
> > restrict it by harmonic bond with metal ion at the active site. 
> > In other words, one of the water molecules to be treated just likes
> > another protein residue by pdb2gmx. How to do that?
> Nobody here owes you an answer. This is a fiddly thing to do, and you 
> will need to work the details out yourself. I can well understand nobody 
> really wanting to get involved. I expect you'd need to
> 1. Add that water to the .gro file by hand after using pdb2gmx, using a 
> residue name distinct from any name other waters might use.
> 2. Extend the protein+metal [ molecule ] section of your .top by hand to 
> add that water, using the information in spc.itp as a model for the 
> stuff you're going to need to make water fit. Also add the harmonic bond 
> in here.
> 3. Then use editconf and/or genbox to generate the rest of the solvent, 
> and massage the [ molecules ] section of your .top to have the 
> appropriate stuff.
> 4. Sacrifice a goat at the full moon.
> Oh, and read Chapter 5 of the manual *really* thoroughly.
> Mark
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  raja_28 at fastmail.us

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