[gmx-users] troubles with zinc ion and distance restraint

[elena.papaleo at unimib.it]

Dear gmx-users,
I'am trying to carry out a minimization, using steepest d., of a protein with
two zinc ion bound.
I try to put distance restraints between the two zinc atoms and the protein
atoms which interact with them using DISRES and I modify the topology file
according to this type of restraints.
When I do the minimization on the protein and distance restraints were applied
only to protein atoms, everything it is ok, but clearly the zinc ions went away.
If I introduce distance restraints on zinc ions and protein atoms, the
minimization stopped at the first step without warning or error message.
Any idea of what I have to do?
Thanks a lot
Elena Papaleo


ps here my file.mdp

title                    = #####
cpp                      = /lib/cpp
include                  = -I../top
define                   = -DDISRES
                                                                                
integrator               = steep
nsteps                   = 1000
nstcomm                  = 1
                                                                                
##### ENERGY MINIMIZATION OPTIONS #####
emtol                    = 100
emstep                   = 0.005
nstlist                  = 10
ns_type                  = grid
##### ENERGY MINIMIZATION OPTIONS #####
                                                                                
rlist                    = 0.9
coulombtype              = PME
rcoulomb                 = 0.9
rvdw                     = 0.9
fourierspacing           = 0.12
pme_order                = 4
ewald_rtol               = 1e-05
                                                                                
disre                    = simple
disre_weighting          = equal
disre_mixed              = no
disre_fc                 = 3000


and the modified .top
                                                                                
#ifdef DISRES
[distance_restraints]
;ai       aj      type    index   type'   low     up1     up2     fac
565      2257       1       0       1       0.350   0.400   0.450   1.0
581      2257       1       1       1       0.350   0.400   0.450   1.0
1087     2257       1       2       1       0.350   0.400   0.450   1.0
1263     2257       1       3       1       0.350   0.400   0.450   1.0
600      2258       1       4       1       0.350   0.400   0.450   1.0
611      2258       1       5       1       0.350   0.400   0.450   1.0
1671     2258       1       6       1       0.350   0.400   0.450   1.0
1263     2258       1       7       1       0.350   0.400   0.450   1.0
#endif