Mon Oct 10 17:02:07 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 17:02:10 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 = 3460 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: 0.6196045 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): 12.37100 62.61900 ymin,ymax (A): -40.93400 10.31400 zmin,zma (A): 28.45700 85.91300 x,y,z range (A): 50.24800 51.24800 57.45600 scale (grids/A): 0.6196045 object centre (A): 37.49500 -15.31000 57.18500 number of atom coordinates read : 3460 total number of charged atoms : 3311 net assigned charge : 3.000040 assigned positive charge : 530.8593 centred at (gu) : 89.48594 90.89965 89.61093 assigned negative charge : -527.8607 centred at (gu) : 89.51405 90.86427 89.66972 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8679 nv = 96 ne = 84 npr = 71379 no. pairs analyzed = 71379 no. exposed pairs = 3851 no. arc points = 26474 no. surface atoms = 1298 nbur = 2162 mkacc time = 0.2000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 519 mr = 5168 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.4300000 number of dielectric boundary points 3963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2792 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 10953 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2116234E-09 -2.7120368E-09 midg,1,midg; midg,igrid,midg -6.7983563E-10 6.6646573E-09 1,midg,midg; igrid,midg,midg 5.3959064E-09 -1.6802187E-10 gauss-seidel spectral radius is 0.9865732 estimated iterations to convergence 71 setup time was (sec) 0.7000000 now iterating at: 17:02:13 rms-change max change #iterations 0.1521892 22.01443 at 10iterations 1.4439454E-02 1.799760 at 20iterations 1.8918975E-03 0.2473125 at 30iterations 6.3026825E-04 8.8062286E-02 at 40iterations 2.8730126E-04 3.7633896E-02 at 50iterations finished qdiffx linear iterations at : 17:02:21 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 2.8730126E-04 3.7633896E-02 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 17:02:23 4.219u 0.278s 0:14.21 31.5% 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 17:02:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3460 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: 1.858814 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): 12.37100 62.61900 ymin,ymax (A): -40.93400 10.31400 zmin,zma (A): 28.45700 85.91300 x,y,z range (A): 50.24800 51.24800 57.45600 scale (grids/A): 1.858814 object centre (A): 37.49500 -15.31000 57.18500 number of atom coordinates read : 3460 total number of charged atoms : 3311 net assigned charge : 3.000040 assigned positive charge : 530.8593 centred at (gu) : 88.45673 92.69797 88.83186 assigned negative charge : -527.8607 centred at (gu) : 88.54163 92.59240 89.00837 start vw surface at 0.1900000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 94422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 35886 mr = 68639 m= 5629 mr = 27334 m= 325 mr = 3498 m= 4 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 2962 time to turn everything in is 0.8400000 number of dielectric boundary points 36666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 25964 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) : 0.6196045 object centre at (A) : 37.49500 -15.31000 57.18500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9658789E-03 -1.3336108E-02 midg,1,midg; midg,igrid,midg 3.4544633E-03 1.6449036E-02 1,midg,midg; igrid,midg,midg 1.0241314E-02 3.1394430E-02 gauss-seidel spectral radius is 0.9986418 estimated iterations to convergence 215 setup time was (sec) 1.140000 now iterating at: 17:02:27 rms-change max change #iterations 4.825818 185.4163 at 10iterations 2.276523 65.74310 at 20iterations 1.071055 29.72042 at 30iterations 0.5042416 13.76872 at 40iterations 0.2381849 6.268066 at 50iterations 0.1121278 3.090998 at 60iterations 5.2780066E-02 1.513299 at 70iterations 2.4996465E-02 0.6882439 at 80iterations 1.1916945E-02 0.3298759 at 90iterations 5.7420852E-03 0.1708086 at 100iterations 2.8959033E-03 8.6326599E-02 at 110iterations 1.5868841E-03 4.4853210E-02 at 120iterations finished qdiffx linear iterations at : 17:02:48 total time elapsed so far: 9.750000 # loops : 120 mean,max change (kT/e) : 1.5868841E-03 4.4853210E-02 energy calculations done at 9.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.910000 DelPhi exited at 17:02:50 9.912u 0.349s 0:24.54 41.7% 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 17:02:50 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 = 3460 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: 2.788220 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): 12.37100 62.61900 ymin,ymax (A): -40.93400 10.31400 zmin,zma (A): 28.45700 85.91300 x,y,z range (A): 50.24800 51.24800 57.45600 scale (grids/A): 2.788220 object centre (A): 37.49500 -15.31000 57.18500 number of atom coordinates read : 3460 total number of charged atoms : 3311 net assigned charge : 3.000040 assigned positive charge : 530.8593 centred at (gu) : 87.68478 94.04685 88.24753 assigned negative charge : -527.8607 centred at (gu) : 87.81230 93.88839 88.51250 start vw surface at 0.1900000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 218698 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 116014 mr = 165799 m= 42310 mr = 96813 m= 9891 mr = 34586 m= 1336 mr = 7400 m= 79 mr = 885 m= 0 mr = 30 time to grow re-entrant surface = 1.330000 no. cavity mid-points inaccessible to solvent = 10343 time to turn everything in is 2.170000 number of dielectric boundary points 82815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 26486 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) : 1.858814 object centre at (A) : 37.49500 -15.31000 57.18500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1523475 -8.0076806E-02 midg,1,midg; midg,igrid,midg -9.3879709E-03 0.2474072 1,midg,midg; igrid,midg,midg 0.1383371 0.4799736 gauss-seidel spectral radius is 0.9992675 estimated iterations to convergence 292 setup time was (sec) 2.500000 now iterating at: 17:02:58 rms-change max change #iterations 11.29576 285.6625 at 10iterations 6.670919 136.8827 at 20iterations 3.910467 83.35109 at 30iterations 2.290512 43.12856 at 40iterations 1.336059 24.75276 at 50iterations 0.7766311 14.57128 at 60iterations 0.4517516 7.812948 at 70iterations 0.2624373 4.604627 at 80iterations 0.1521972 2.914825 at 90iterations 8.8118576E-02 1.607160 at 100iterations 5.1190447E-02 0.8862019 at 110iterations 2.9652715E-02 0.5382156 at 120iterations 1.7268015E-02 0.2825010 at 130iterations 1.0053881E-02 0.1623840 at 140iterations 5.9019267E-03 9.4359398E-02 at 150iterations 3.5184494E-03 6.3795090E-02 at 160iterations 2.1652551E-03 3.9079666E-02 at 170iterations 1.4064235E-03 2.4114609E-02 at 180iterations finished qdiffx linear iterations at : 17:03:25 total time elapsed so far: 17.20000 # loops : 180 mean,max change (kT/e) : 1.4064235E-03 2.4114609E-02 energy calculations done at 17.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.39000 DelPhi exited at 17:03:26 17.395u 0.363s 0:35.49 50.0% 0+0k 0+0io 0pf+0w