Sun Oct 9 12:45:54 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 Sun Oct 9 2011 at 12:45:54 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 = 2395 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6943767 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): -6.050000 44.04500 ymin,ymax (A): -1.008000 50.26100 zmin,zma (A): 34.33300 75.88300 x,y,z range (A): 50.09500 51.26900 41.55000 scale (grids/A): 0.6943767 object centre (A): 18.99750 24.62650 55.10800 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 2.500025 assigned positive charge : 366.2230 centred at (gu) : 89.59728 88.86382 89.37350 assigned negative charge : -363.7236 centred at (gu) : 89.59949 88.66033 89.32854 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7632 nv = 96 ne = 84 npr = 48589 no. pairs analyzed = 48589 no. exposed pairs = 2917 no. arc points = 20218 no. surface atoms = 976 nbur = 1419 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 492 mr = 4278 m= 5 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1922 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0713341E-09 3.1684415E-08 midg,1,midg; midg,igrid,midg -9.1244551E-08 8.1245609E-08 1,midg,midg; igrid,midg,midg 1.9094864E-08 1.4605866E-08 gauss-seidel spectral radius is 0.9892219 estimated iterations to convergence 78 setup time was (sec) 0.5300000 now iterating at: 12:45:55 rms-change max change #iterations 0.1978220 28.16241 at 10iterations 2.3952421E-02 3.975942 at 20iterations 3.1754852E-03 0.4233236 at 30iterations 5.9627555E-04 0.1032333 at 40iterations 1.6789456E-04 2.7803421E-02 at 50iterations finished qdiffx linear iterations at : 12:45:58 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.6789456E-04 2.7803421E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 12:45:58 3.363u 0.172s 0:03.80 92.8% 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 Sun Oct 9 2011 at 12:45:58 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 = 2395 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.083130 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): -6.050000 44.04500 ymin,ymax (A): -1.008000 50.26100 zmin,zma (A): 34.33300 75.88300 x,y,z range (A): 50.09500 51.26900 41.55000 scale (grids/A): 2.083130 object centre (A): 18.99750 24.62650 55.10800 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 2.500025 assigned positive charge : 366.2230 centred at (gu) : 88.79150 86.59083 88.12029 assigned negative charge : -363.7236 centred at (gu) : 88.79827 85.98085 87.98557 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81652 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20218 grid for indexing accessible points = 1.400000 m= 31271 mr = 57339 m= 5672 mr = 23390 m= 541 mr = 3672 m= 12 mr = 284 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 103 time to turn everything in is 0.6100000 number of dielectric boundary points 34461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17870 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) : 0.6943767 object centre at (A) : 18.99750 24.62650 55.10800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4773950E-03 4.2632975E-02 midg,1,midg; midg,igrid,midg -7.5458534E-02 2.0156216E-02 1,midg,midg; igrid,midg,midg 4.9574807E-02 1.2698120E-03 gauss-seidel spectral radius is 0.9988253 estimated iterations to convergence 231 setup time was (sec) 0.9100000 now iterating at: 12:45:59 rms-change max change #iterations 4.885306 254.2607 at 10iterations 2.407846 89.71210 at 20iterations 1.191705 38.76044 at 30iterations 0.5905324 18.45625 at 40iterations 0.2922924 8.799469 at 50iterations 0.1451410 4.137508 at 60iterations 7.1558781E-02 1.917349 at 70iterations 3.5701588E-02 1.022268 at 80iterations 1.7793601E-02 0.6099358 at 90iterations 8.9124870E-03 0.2737284 at 100iterations 4.4742208E-03 0.1376264 at 110iterations 2.3161946E-03 7.1998596E-02 at 120iterations finished qdiffx linear iterations at : 12:46:06 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 2.3161946E-03 7.1998596E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 12:46:06 7.604u 0.169s 0:08.04 96.5% 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 Sun Oct 9 2011 at 12:46:06 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 = 2395 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: 3.124695 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): -6.050000 44.04500 ymin,ymax (A): -1.008000 50.26100 zmin,zma (A): 34.33300 75.88300 x,y,z range (A): 50.09500 51.26900 41.55000 scale (grids/A): 3.124695 object centre (A): 18.99750 24.62650 55.10800 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 2.500025 assigned positive charge : 366.2230 centred at (gu) : 88.18707 84.88612 87.18022 assigned negative charge : -363.7236 centred at (gu) : 88.19737 83.97119 86.97826 start vw surface at 0.1500000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 188714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20218 grid for indexing accessible points = 1.400000 m= 98759 mr = 138673 m= 38113 mr = 81633 m= 10412 mr = 30784 m= 2200 mr = 7876 m= 264 mr = 1688 m= 6 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 281 time to turn everything in is 1.950000 number of dielectric boundary points 77650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 18024 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) : 2.083130 object centre at (A) : 18.99750 24.62650 55.10800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7024676E-02 0.4501057 midg,1,midg; midg,igrid,midg -0.7652153 0.4276130 1,midg,midg; igrid,midg,midg 0.5365595 -0.1781998 gauss-seidel spectral radius is 0.9992968 estimated iterations to convergence 298 setup time was (sec) 2.260000 now iterating at: 12:46:09 rms-change max change #iterations 10.95572 359.7599 at 10iterations 6.486385 121.1566 at 20iterations 3.825701 69.21690 at 30iterations 2.260925 41.85723 at 40iterations 1.334008 23.44538 at 50iterations 0.7820227 14.34345 at 60iterations 0.4597745 8.819315 at 70iterations 0.2694936 5.280254 at 80iterations 0.1577627 2.849197 at 90iterations 9.2540532E-02 1.658777 at 100iterations 5.4231469E-02 0.8546791 at 110iterations 3.1873655E-02 0.5234258 at 120iterations 1.8899148E-02 0.3226318 at 130iterations 1.1282813E-02 0.2220535 at 140iterations 6.8887314E-03 0.1288128 at 150iterations 4.3575251E-03 8.2717896E-02 at 160iterations 2.8874530E-03 6.5895081E-02 at 170iterations 2.0402756E-03 4.6455383E-02 at 180iterations finished qdiffx linear iterations at : 12:46:19 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 2.0402756E-03 4.6455383E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 12:46:19 12.891u 0.167s 0:13.32 97.9% 0+0k 0+0io 0pf+0w