Sat Oct 8 14:29:03 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 Sat Oct 8 2011 at 14:29:03 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3052 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6323830 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): -11.85100 43.45100 ymin,ymax (A): -22.32000 22.28700 zmin,zma (A): -8.093000 48.20200 x,y,z range (A): 55.30200 44.60700 56.29500 scale (grids/A): 0.6323830 object centre (A): 15.80000 -1.6500473E-02 20.05450 number of atom coordinates read : 3052 total number of charged atoms : 2905 net assigned charge : 1.000006 assigned positive charge : 458.0356 centred at (gu) : 88.71543 89.57107 91.61841 assigned negative charge : -457.0363 centred at (gu) : 88.70332 89.50078 91.54535 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7927 nv = 96 ne = 84 npr = 64674 no. pairs analyzed = 64674 no. exposed pairs = 3426 no. arc points = 24041 no. surface atoms = 1169 nbur = 1883 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 446 mr = 4637 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2379 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9603224E-09 1.3032614E-08 midg,1,midg; midg,igrid,midg -7.4562747E-09 8.0200344E-09 1,midg,midg; igrid,midg,midg -3.7935424E-10 1.8377022E-09 gauss-seidel spectral radius is 0.9870778 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 14:29:03 rms-change max change #iterations 0.1543262 25.50958 at 10iterations 1.5156010E-02 2.107859 at 20iterations 1.5567128E-03 0.2107553 at 30iterations 1.9284726E-04 2.2925854E-02 at 40iterations 3.1479420E-05 4.0893555E-03 at 50iterations finished qdiffx linear iterations at : 14:29:07 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 3.1479420E-05 4.0893555E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 14:29:07 4.235u 0.233s 0:04.77 93.5% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 14:29:07 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3052 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.897149 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): -11.85100 43.45100 ymin,ymax (A): -22.32000 22.28700 zmin,zma (A): -8.093000 48.20200 x,y,z range (A): 55.30200 44.60700 56.29500 scale (grids/A): 1.897149 object centre (A): 15.80000 -1.6500473E-02 20.05450 number of atom coordinates read : 3052 total number of charged atoms : 2905 net assigned charge : 1.000006 assigned positive charge : 458.0356 centred at (gu) : 86.14597 88.71271 94.85487 assigned negative charge : -457.0363 centred at (gu) : 86.10965 88.50206 94.63570 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 86910 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24041 grid for indexing accessible points = 1.400000 m= 31373 mr = 62688 m= 4700 mr = 23577 m= 290 mr = 2865 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 394 time to turn everything in is 0.6500000 number of dielectric boundary points 34068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 22865 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) : 0.6323830 object centre at (A) : 15.80000 -1.6500473E-02 20.05450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6363325E-02 2.7380034E-02 midg,1,midg; midg,igrid,midg 6.4276960E-03 1.7156119E-02 1,midg,midg; igrid,midg,midg -4.9130943E-02 3.7686417E-03 gauss-seidel spectral radius is 0.9986582 estimated iterations to convergence 216 setup time was (sec) 0.9900000 now iterating at: 14:29:09 rms-change max change #iterations 4.639383 204.9067 at 10iterations 2.195821 69.46867 at 20iterations 1.036781 30.03338 at 30iterations 0.4884992 14.30288 at 40iterations 0.2312443 7.192308 at 50iterations 0.1093754 3.144654 at 60iterations 5.1616948E-02 1.535141 at 70iterations 2.4306461E-02 0.7431707 at 80iterations 1.1540309E-02 0.3258553 at 90iterations 5.4620015E-03 0.1660843 at 100iterations 2.6023111E-03 7.5811386E-02 at 110iterations 1.2275082E-03 3.3920288E-02 at 120iterations finished qdiffx linear iterations at : 14:29:17 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 1.2275082E-03 3.3920288E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 14:29:18 9.734u 0.242s 0:10.26 97.1% 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 Sat Oct 8 2011 at 14:29:18 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3052 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.845724 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): -11.85100 43.45100 ymin,ymax (A): -22.32000 22.28700 zmin,zma (A): -8.093000 48.20200 x,y,z range (A): 55.30200 44.60700 56.29500 scale (grids/A): 2.845724 object centre (A): 15.80000 -1.6500473E-02 20.05450 number of atom coordinates read : 3052 total number of charged atoms : 2905 net assigned charge : 1.000006 assigned positive charge : 458.0356 centred at (gu) : 84.21884 88.06876 97.28220 assigned negative charge : -457.0363 centred at (gu) : 84.16454 87.75300 96.95345 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 201465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24041 grid for indexing accessible points = 1.400000 m= 102583 mr = 151679 m= 36226 mr = 85257 m= 8381 mr = 29219 m= 1179 mr = 6127 m= 62 mr = 764 m= 0 mr = 17 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 1296 time to turn everything in is 1.670000 number of dielectric boundary points 76833 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 23239 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) : 1.897149 object centre at (A) : 15.80000 -1.6500473E-02 20.05450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.2080225E-02 0.5221685 midg,1,midg; midg,igrid,midg 7.1461909E-02 0.1993186 1,midg,midg; igrid,midg,midg -0.8331161 0.1050164 gauss-seidel spectral radius is 0.9992680 estimated iterations to convergence 292 setup time was (sec) 2.030000 now iterating at: 14:29:20 rms-change max change #iterations 10.84496 381.3110 at 10iterations 6.357583 145.8405 at 20iterations 3.706625 67.96607 at 30iterations 2.154385 40.51207 at 40iterations 1.249926 25.39079 at 50iterations 0.7236044 12.59591 at 60iterations 0.4192048 7.329767 at 70iterations 0.2425555 4.607790 at 80iterations 0.1400747 2.350071 at 90iterations 8.0928043E-02 1.387753 at 100iterations 4.6870794E-02 0.8026347 at 110iterations 2.7016034E-02 0.4653616 at 120iterations 1.5609741E-02 0.2823639 at 130iterations 9.0341736E-03 0.1656079 at 140iterations 5.2209678E-03 9.0583801E-02 at 150iterations 3.0280347E-03 5.0071716E-02 at 160iterations 1.7589829E-03 2.8837204E-02 at 170iterations 1.0303803E-03 1.6972542E-02 at 180iterations finished qdiffx linear iterations at : 14:29:34 total time elapsed so far: 15.67000 # loops : 180 mean,max change (kT/e) : 1.0303803E-03 1.6972542E-02 energy calculations done at 15.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.85000 DelPhi exited at 14:29:34 15.851u 0.267s 0:16.41 98.1% 0+0k 0+0io 0pf+0w