[gmx-users] Re: Internal water in the membrane receptor
Mark.Abraham at anu.edu.au
Mon Feb 27 12:30:59 CET 2012
On 27/02/2012 8:35 PM, James Starlight wrote:
> 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
> 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
> integrator = steep ; Algorithm (steep = steepest descent
> 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 ?
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