Mon Oct 10 14:12:19 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+sph2.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 = amb2.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 14:12:20 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6276667 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): -11.98000 43.52500 ymin,ymax (A): -10.64700 46.07100 zmin,zma (A): -27.86500 20.00600 x,y,z range (A): 55.50500 56.71800 47.87100 scale (grids/A): 0.6276667 object centre (A): 15.77250 17.71200 -3.929500 number of atom coordinates read : 2558 total number of charged atoms : 2384 net assigned charge : 3.500013 assigned positive charge : 381.3829 centred at (gu) : 89.39980 90.01690 91.17422 assigned negative charge : -377.8834 centred at (gu) : 89.42466 90.06149 91.12337 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7014 nv = 96 ne = 84 npr = 50310 no. pairs analyzed = 50310 no. exposed pairs = 3380 no. arc points = 24842 no. surface atoms = 1125 nbur = 1433 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 3644 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2430 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5406140E-10 9.7586277E-09 midg,1,midg; midg,igrid,midg 7.0285480E-09 -1.2866963E-10 1,midg,midg; igrid,midg,midg 6.2335754E-09 1.3118449E-09 gauss-seidel spectral radius is 0.9868591 estimated iterations to convergence 71 setup time was (sec) 0.6900000 now iterating at: 14:12:20 rms-change max change #iterations 0.1330093 21.00698 at 10iterations 1.2243201E-02 1.787575 at 20iterations 1.1725696E-03 0.1745443 at 30iterations 1.1021927E-04 1.6204834E-02 at 40iterations 1.0736251E-05 1.5411377E-03 at 50iterations finished qdiffx linear iterations at : 14:12:24 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 1.0736251E-05 1.5411377E-03 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 14:12:25 4.403u 0.251s 0:05.21 89.2% 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 14:12:25 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.883000 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): -11.98000 43.52500 ymin,ymax (A): -10.64700 46.07100 zmin,zma (A): -27.86500 20.00600 x,y,z range (A): 55.50500 56.71800 47.87100 scale (grids/A): 1.883000 object centre (A): 15.77250 17.71200 -3.929500 number of atom coordinates read : 2558 total number of charged atoms : 2384 net assigned charge : 3.500013 assigned positive charge : 381.3829 centred at (gu) : 88.19906 90.05046 93.52211 assigned negative charge : -377.8834 centred at (gu) : 88.27364 90.18417 93.37001 start vw surface at 0.2200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 74853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24842 grid for indexing accessible points = 1.400000 m= 27354 mr = 50512 m= 4401 mr = 19647 m= 254 mr = 2481 m= 1 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 125 time to turn everything in is 0.7400000 number of dielectric boundary points 34134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 18679 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) : 0.6276667 object centre at (A) : 15.77250 17.71200 -3.929500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0450908E-04 2.6338598E-02 midg,1,midg; midg,igrid,midg 1.3852176E-03 2.5319289E-02 1,midg,midg; igrid,midg,midg 1.1760456E-02 -6.3649230E-03 gauss-seidel spectral radius is 0.9986112 estimated iterations to convergence 213 setup time was (sec) 1.100000 now iterating at: 14:12:26 rms-change max change #iterations 4.170309 187.0912 at 10iterations 1.931456 72.80461 at 20iterations 0.8991379 30.91396 at 30iterations 0.4174780 13.45465 at 40iterations 0.1931556 6.403481 at 50iterations 8.9801110E-02 2.876686 at 60iterations 4.1825626E-02 1.451260 at 70iterations 1.9392490E-02 0.6433239 at 80iterations 9.0643447E-03 0.3018697 at 90iterations 4.1885511E-03 0.1347437 at 100iterations 1.9544759E-03 7.0529938E-02 at 110iterations 9.1126573E-04 2.8819084E-02 at 120iterations finished qdiffx linear iterations at : 14:12:34 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 9.1126573E-04 2.8819084E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 14:12:35 9.604u 0.226s 0:10.45 93.9% 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 14:12:35 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.824500 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): -11.98000 43.52500 ymin,ymax (A): -10.64700 46.07100 zmin,zma (A): -27.86500 20.00600 x,y,z range (A): 55.50500 56.71800 47.87100 scale (grids/A): 2.824500 object centre (A): 15.77250 17.71200 -3.929500 number of atom coordinates read : 2558 total number of charged atoms : 2384 net assigned charge : 3.500013 assigned positive charge : 381.3829 centred at (gu) : 87.29833 90.07549 95.28301 assigned negative charge : -377.8834 centred at (gu) : 87.41041 90.27621 95.05510 start vw surface at 0.1900000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 172626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24842 grid for indexing accessible points = 1.400000 m= 87762 mr = 122665 m= 32146 mr = 70514 m= 7746 mr = 25057 m= 1106 mr = 5482 m= 70 mr = 704 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 366 time to turn everything in is 1.810000 number of dielectric boundary points 77018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 19070 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) : 1.883000 object centre at (A) : 15.77250 17.71200 -3.929500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6742093E-04 0.3304768 midg,1,midg; midg,igrid,midg 1.9319125E-02 0.4827816 1,midg,midg; igrid,midg,midg 0.1132495 1.7179059E-02 gauss-seidel spectral radius is 0.9992572 estimated iterations to convergence 290 setup time was (sec) 2.170000 now iterating at: 14:12:38 rms-change max change #iterations 9.833926 355.5568 at 10iterations 5.816617 161.8018 at 20iterations 3.396201 81.14371 at 30iterations 1.978911 46.76429 at 40iterations 1.150085 22.48940 at 50iterations 0.6655074 14.82555 at 60iterations 0.3846650 7.991089 at 70iterations 0.2218092 4.455780 at 80iterations 0.1279242 2.441996 at 90iterations 7.3613480E-02 1.428070 at 100iterations 4.2393491E-02 0.7588682 at 110iterations 2.4354750E-02 0.4587135 at 120iterations 1.4002783E-02 0.2455177 at 130iterations 8.0414563E-03 0.1608011 at 140iterations 4.6219635E-03 8.8654518E-02 at 150iterations 2.6480351E-03 5.3534031E-02 at 160iterations 1.5235054E-03 2.7496338E-02 at 170iterations 8.7443681E-04 1.5609741E-02 at 180iterations finished qdiffx linear iterations at : 14:12:51 total time elapsed so far: 15.37000 # loops : 180 mean,max change (kT/e) : 8.7443681E-04 1.5609741E-02 energy calculations done at 15.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.60000 DelPhi exited at 14:12:52 15.604u 0.216s 0:16.33 96.8% 0+0k 0+0io 0pf+0w