[gmx-users] Including water in for restraining

[raja]

Hi Chris,
Thanks for your detailed message and it is very helpful.

B.Nataraj



On Wed, 15 Nov 2006 22:01:32 -0500, chris.neale at utoronto.ca said:
> you are correct that you must include the water as part of the same  
> molecule (as you appear to have already done for Zn). I assume that  
> protein_ion_A.itp contains only one [ moleculetypes ] section that has  
> the protein and also the zinc. Take a look at how Zn has been included  
> there. Repeat this procedure to include the water that you want to be  
> bonded. Then modify your coordinate file accordingly. You can get  
> water parameters from gromacs-3.3.1/share/gromacs/top/tip3p.itp (or  
> sub the name of your favourite water model).
> 
> Note that this is intended as my best idea about how to go about doing  
> exactly what you have asked. I have no idea how this is going to  
> affect things like a temperature group that contains a protein, a  
> zinc, and a single water if you have multiple temperature coupling  
> groups. Also I am not sure if settle is going to work properly.
> 
> There is no warranty associated with this next portion, I have never  
> tried it. I have included this just to be explicit about what I am  
> suggesting. Lets say you use tip4p and oplsaa:
> 
> under [ atoms ] add:
> 2901       opls_113        1       SOL      OW     1       0.0
> 2902       opls_114        1       SOL     HW1     1       0.52
> 2903       opls_114        1       SOL     HW2     1       0.52
> 2904       opls_115        1       SOL      MW     1      -1.04
> 
> under [ bonds ] add:
> #ifdef FLEXIBLE
> ; i     j       funct   length  force.c.
> 2901       2902       2901       0.09572 502416.0 0.09572        502416.0
> 2901       2903       2901       0.09572 502416.0 0.09572        502416.0
> #endif
> 
> under [ angles ] add:
> #ifdef FLEXIBLE
> ; i     j       k       funct   angle   force.c.
> 2902       2901       2903       1       104.52  628.02  104.52  628.02
> #else
> [ settles ]
> ; OW    funct   doh        dhh
> 2901       1       0.09572    0.15139
> #endif
> 
> Then also add:
> [ exclusions ]
> 2901       2902       2903       2904
> 2902       2901       2903       2904
> 2903       2901       2902       2904
> 2904       2901       2902       2903
> 
> [ dummies3 ]
> ; Dummy from                    funct   a               b
> 2904       2901       2902       2903       1       0.128012065      
> 0.128012065
> 
> 
> Then go back and add any bonds that you want between this water and  
> the protein or zinc.
> 
> It is unclear to me if the [ exclusions ] section is necessary or even  
> advisable.
> 
> 
> 
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  raja
  raja_28 at fastmail.us

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