Sat Oct 8 15:52:30 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 Sat Oct 8 2011 at 15:52:30 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2338 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 0.6566448 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): -2.139000 46.45300 ymin,ymax (A): -16.96200 29.55400 zmin,zma (A): -17.97200 36.24300 x,y,z range (A): 48.59200 46.51600 54.21500 scale (grids/A): 0.6566448 object centre (A): 22.15700 6.296000 9.135500 number of atom coordinates read : 2338 total number of charged atoms : 2252 net assigned charge : 1.900003 assigned positive charge : 348.3181 centred at (gu) : 90.24033 88.82837 90.08894 assigned negative charge : -346.4188 centred at (gu) : 90.22874 88.93843 90.18923 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6777 nv = 96 ne = 84 npr = 47449 no. pairs analyzed = 47449 no. exposed pairs = 2880 no. arc points = 19971 no. surface atoms = 985 nbur = 1353 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 3789 m= 4 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2600000 number of dielectric boundary points 3328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2003 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8146 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9884672E-08 -1.2448148E-08 midg,1,midg; midg,igrid,midg 2.7970763E-08 -1.0737774E-08 1,midg,midg; igrid,midg,midg 2.2170696E-09 6.3797376E-09 gauss-seidel spectral radius is 0.9879580 estimated iterations to convergence 74 setup time was (sec) 0.5100000 now iterating at: 15:52:31 rms-change max change #iterations 0.1555852 26.32495 at 10iterations 1.6096700E-02 2.062744 at 20iterations 1.7383941E-03 0.2500515 at 30iterations 2.0213817E-04 2.6852608E-02 at 40iterations 3.0126494E-05 4.7407150E-03 at 50iterations finished qdiffx linear iterations at : 15:52:34 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 3.0126494E-05 4.7407150E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 15:52:34 3.311u 0.193s 0:03.79 92.3% 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 Sat Oct 8 2011 at 15:52:34 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2338 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 1.969934 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): -2.139000 46.45300 ymin,ymax (A): -16.96200 29.55400 zmin,zma (A): -17.97200 36.24300 x,y,z range (A): 48.59200 46.51600 54.21500 scale (grids/A): 1.969934 object centre (A): 22.15700 6.296000 9.135500 number of atom coordinates read : 2338 total number of charged atoms : 2252 net assigned charge : 1.900003 assigned positive charge : 348.3181 centred at (gu) : 90.72052 86.48448 90.26644 assigned negative charge : -346.4188 centred at (gu) : 90.68626 86.81525 90.56777 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19971 grid for indexing accessible points = 1.400000 m= 26812 mr = 51386 m= 4834 mr = 20066 m= 341 mr = 3219 m= 7 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 762 time to turn everything in is 0.5500000 number of dielectric boundary points 30458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17780 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) : 0.6566448 object centre at (A) : 22.15700 6.296000 9.135500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2906506E-02 -2.3190735E-02 midg,1,midg; midg,igrid,midg 2.4371577E-02 -8.4123053E-03 1,midg,midg; igrid,midg,midg -3.7616624E-03 -4.3775108E-02 gauss-seidel spectral radius is 0.9986947 estimated iterations to convergence 219 setup time was (sec) 0.8500000 now iterating at: 15:52:35 rms-change max change #iterations 4.282878 196.2410 at 10iterations 2.028468 84.54814 at 20iterations 0.9631653 31.20856 at 30iterations 0.4601446 13.70554 at 40iterations 0.2188054 7.442498 at 50iterations 0.1045127 3.082402 at 60iterations 4.9675379E-02 1.480145 at 70iterations 2.3680802E-02 0.7680807 at 80iterations 1.1271999E-02 0.3610134 at 90iterations 5.3680222E-03 0.1609116 at 100iterations 2.5791063E-03 7.6217651E-02 at 110iterations 1.2250505E-03 3.7854195E-02 at 120iterations finished qdiffx linear iterations at : 15:52:42 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 1.2250505E-03 3.7854195E-02 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 15:52:42 7.559u 0.214s 0:08.13 95.4% 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 15:52:42 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2338 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 2.954902 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): -2.139000 46.45300 ymin,ymax (A): -16.96200 29.55400 zmin,zma (A): -17.97200 36.24300 x,y,z range (A): 48.59200 46.51600 54.21500 scale (grids/A): 2.954902 object centre (A): 22.15700 6.296000 9.135500 number of atom coordinates read : 2338 total number of charged atoms : 2252 net assigned charge : 1.900003 assigned positive charge : 348.3181 centred at (gu) : 91.08070 84.72666 90.39954 assigned negative charge : -346.4188 centred at (gu) : 91.02939 85.22287 90.85162 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 169738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19971 grid for indexing accessible points = 1.400000 m= 85573 mr = 124440 m= 32712 mr = 70493 m= 9087 mr = 26828 m= 1489 mr = 7119 m= 119 mr = 1061 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 2651 time to turn everything in is 1.340000 number of dielectric boundary points 68719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 18016 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) : 1.969934 object centre at (A) : 22.15700 6.296000 9.135500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2891426 -0.2966954 midg,1,midg; midg,igrid,midg 0.2008497 -0.1222127 1,midg,midg; igrid,midg,midg -4.9513724E-02 -0.6640172 gauss-seidel spectral radius is 0.9992700 estimated iterations to convergence 292 setup time was (sec) 1.650000 now iterating at: 15:52:44 rms-change max change #iterations 9.890655 552.0876 at 10iterations 5.795271 129.1223 at 20iterations 3.389877 73.18154 at 30iterations 1.977393 39.04233 at 40iterations 1.148181 21.39999 at 50iterations 0.6661855 13.81114 at 60iterations 0.3866692 7.720329 at 70iterations 0.2240453 4.046288 at 80iterations 0.1296674 2.322774 at 90iterations 7.5083442E-02 1.330126 at 100iterations 4.3385882E-02 0.8209496 at 110iterations 2.5082173E-02 0.4203315 at 120iterations 1.4474004E-02 0.2862053 at 130iterations 8.3526568E-03 0.1695023 at 140iterations 4.8295166E-03 7.7278137E-02 at 150iterations 2.7861996E-03 5.0009012E-02 at 160iterations 1.6054454E-03 2.7378082E-02 at 170iterations 9.2886545E-04 1.6605377E-02 at 180iterations finished qdiffx linear iterations at : 15:52:55 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 9.2886545E-04 1.6605377E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 15:52:55 12.331u 0.238s 0:12.93 97.1% 0+0k 0+0io 0pf+0w