[gmx-users] Re: Internal water in the membrane receptor

[Mark Abraham]

On 27/02/2012 8:35 PM, James Starlight wrote:
> Mark,
>
> I've found a possible sollution to restrict oxygens of my X-ray water 
> by possible plasing the below string in the TOPOLOGY.top of my system
>
> ; Include X-ray water topology
> #include "XW.itp"
>
> ; Include Position restraint file
> #ifdef POSRES_XW
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> I havent recieved any errors from gromp. Does this aproach correct in 
> general ?

Yes. There's only one heavy atom in a water, so that's all you need to 
restrain. You want it to have rotational freedom for EM, of course.

>
> I dont know why but after minimisation constrained mollecules were 
> diffused from the protein interious so POSRES have not worked :(

That's sterically impossible with or without position restraints. Either 
you're looking at the wrong before-and-after files, or the after file 
has some periodicity artefact in your viewing program. If you set 
nstxout = 1 then you can watch the EM process step by step.

>
> My minim.mdp consist of two separate posres for water as well as for 
> ligand groups ( there are no posre for protein).
>
>
> define        = -DPOSRES_LIG -DPOSRES_XW    ; position restrain the 
> protein
> integrator    = steep        ; Algorithm (steep = steepest descent 
> minimization)
> emtol        = 1000.0      ; Stop minimization when the maximum force 
> < 1000.0 kJ/mol/nm
> emstep      = 0.01      ; Energy step size
> nsteps        = 50000          ; Maximum number of (minimization) 
> steps to perform
> energygrps = Protein CAR
>
> What should I add to that file to activate posres?
> Finally are the constraints algorithm needed here ?
>
>
> James
>
>

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