Mon Oct 10 13:54:36 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 13:54:36 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2296 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6500620 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 5.509000 60.27300 ymin,ymax (A): -9.340000 33.28800 zmin,zma (A): -12.89100 41.05300 x,y,z range (A): 54.76400 42.62800 53.94400 scale (grids/A): 0.6500620 object centre (A): 32.89100 11.97400 14.08100 number of atom coordinates read : 2296 total number of charged atoms : 2162 net assigned charge : 11.50002 assigned positive charge : 333.0246 centred at (gu) : 91.52612 91.48432 89.20973 assigned negative charge : -321.5252 centred at (gu) : 91.50677 91.41496 89.19379 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6773 nv = 96 ne = 84 npr = 45447 no. pairs analyzed = 45447 no. exposed pairs = 3031 no. arc points = 22006 no. surface atoms = 1014 nbur = 1282 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 3493 m= 6 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3200000 number of dielectric boundary points 3654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2198 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7870 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3429914E-08 2.0413104E-08 midg,1,midg; midg,igrid,midg 9.8770290E-09 4.1752998E-08 1,midg,midg; igrid,midg,midg 1.4388796E-08 3.3433075E-08 gauss-seidel spectral radius is 0.9877215 estimated iterations to convergence 74 setup time was (sec) 0.6000000 now iterating at: 13:54:37 rms-change max change #iterations 0.1380438 22.34111 at 10iterations 1.4425601E-02 1.961142 at 20iterations 1.5700990E-03 0.2181969 at 30iterations 2.1495728E-04 3.9541245E-02 at 40iterations 4.0539384E-05 8.1405640E-03 at 50iterations finished qdiffx linear iterations at : 13:54:40 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 4.0539384E-05 8.1405640E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 13:54:41 4.058u 0.239s 0:04.79 89.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 13:54:41 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2296 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.950186 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 5.509000 60.27300 ymin,ymax (A): -9.340000 33.28800 zmin,zma (A): -12.89100 41.05300 x,y,z range (A): 54.76400 42.62800 53.94400 scale (grids/A): 1.950186 object centre (A): 32.89100 11.97400 14.08100 number of atom coordinates read : 2296 total number of charged atoms : 2162 net assigned charge : 11.50002 assigned positive charge : 333.0246 centred at (gu) : 94.57825 94.45251 87.62878 assigned negative charge : -321.5252 centred at (gu) : 94.52061 94.24496 87.58144 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 72184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22006 grid for indexing accessible points = 1.400000 m= 26873 mr = 48237 m= 4917 mr = 19481 m= 399 mr = 3068 m= 13 mr = 174 m= 0 mr = 2 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 33424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17074 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6500620 object centre at (A) : 32.89100 11.97400 14.08100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4061388E-02 4.4625655E-02 midg,1,midg; midg,igrid,midg 2.0087329E-03 3.0793115E-02 1,midg,midg; igrid,midg,midg 4.5894671E-02 2.8786248E-02 gauss-seidel spectral radius is 0.9986761 estimated iterations to convergence 218 setup time was (sec) 0.9500000 now iterating at: 13:54:42 rms-change max change #iterations 3.979675 168.1892 at 10iterations 1.881776 74.86972 at 20iterations 0.8877556 34.31484 at 30iterations 0.4195848 14.87745 at 40iterations 0.1993045 6.411034 at 50iterations 9.4073676E-02 2.998066 at 60iterations 4.4503387E-02 1.448648 at 70iterations 2.1095298E-02 0.6670809 at 80iterations 9.9969860E-03 0.3044834 at 90iterations 4.7433698E-03 0.1649513 at 100iterations 2.2656028E-03 6.7541122E-02 at 110iterations 1.0846064E-03 3.4305573E-02 at 120iterations finished qdiffx linear iterations at : 13:54:50 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 1.0846064E-03 3.4305573E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 13:54:51 9.433u 0.309s 0:10.11 96.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 13:54:51 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2296 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.925279 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 5.509000 60.27300 ymin,ymax (A): -9.340000 33.28800 zmin,zma (A): -12.89100 41.05300 x,y,z range (A): 54.76400 42.62800 53.94400 scale (grids/A): 2.925279 object centre (A): 32.89100 11.97400 14.08100 number of atom coordinates read : 2296 total number of charged atoms : 2162 net assigned charge : 11.50002 assigned positive charge : 333.0246 centred at (gu) : 96.86732 96.67873 86.44312 assigned negative charge : -321.5252 centred at (gu) : 96.78098 96.36743 86.37223 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 166102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22006 grid for indexing accessible points = 1.400000 m= 84715 mr = 116993 m= 33161 mr = 68186 m= 8975 mr = 26392 m= 1588 mr = 6722 m= 184 mr = 1106 m= 5 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.710000 number of dielectric boundary points 75227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 17296 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.950186 object centre at (A) : 32.89100 11.97400 14.08100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6170253 0.4012059 midg,1,midg; midg,igrid,midg 2.0994660E-02 0.2919084 1,midg,midg; igrid,midg,midg 0.6042559 0.2825650 gauss-seidel spectral radius is 0.9992779 estimated iterations to convergence 294 setup time was (sec) 2.040000 now iterating at: 13:54:53 rms-change max change #iterations 9.552501 432.7030 at 10iterations 5.671758 144.7012 at 20iterations 3.346726 77.44305 at 30iterations 1.963841 52.14113 at 40iterations 1.150088 23.96592 at 50iterations 0.6722779 14.48067 at 60iterations 0.3924638 8.190054 at 70iterations 0.2278676 4.570923 at 80iterations 0.1325466 2.622204 at 90iterations 7.7078767E-02 1.649504 at 100iterations 4.4675894E-02 1.026871 at 110iterations 2.5971048E-02 0.5133960 at 120iterations 1.5058639E-02 0.2791843 at 130iterations 8.7138563E-03 0.1731033 at 140iterations 5.0660153E-03 9.3122482E-02 at 150iterations 2.9499223E-03 5.3680420E-02 at 160iterations 1.7164139E-03 3.2068253E-02 at 170iterations 1.0039763E-03 1.8939972E-02 at 180iterations finished qdiffx linear iterations at : 13:55:07 total time elapsed so far: 15.75000 # loops : 180 mean,max change (kT/e) : 1.0039763E-03 1.8939972E-02 energy calculations done at 15.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.92000 DelPhi exited at 13:55:08 15.921u 0.308s 0:16.80 96.5% 0+0k 0+0io 0pf+0w