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

James Starlight jmsstarlight at gmail.com
Mon Feb 27 10:35:45 CET 2012


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 ?

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

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
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
energygrps = Protein CAR

What should I add to that file to activate posres?
Finally are the constraints algorithm needed here ?

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