Sun Oct 9 14:06:04 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 Sun Oct 9 2011 at 14:06:04 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2387 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 0.6867151 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): 21.44000 70.61600 ymin,ymax (A): -1.765000 50.07600 zmin,zma (A): -5.665000 37.15800 x,y,z range (A): 49.17599 51.84100 42.82300 scale (grids/A): 0.6867151 object centre (A): 46.02800 24.15550 15.74650 number of atom coordinates read : 2387 total number of charged atoms : 2241 net assigned charge : 3.406023 assigned positive charge : 366.6511 centred at (gu) : 90.36454 89.05093 89.10445 assigned negative charge : -363.2455 centred at (gu) : 90.39018 88.90182 89.01534 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7587 nv = 96 ne = 84 npr = 48055 no. pairs analyzed = 48055 no. exposed pairs = 2849 no. arc points = 20650 no. surface atoms = 961 nbur = 1426 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4258 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2900000 number of dielectric boundary points 3720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1934 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8683 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6802399E-08 4.1662439E-08 midg,1,midg; midg,igrid,midg -4.3688427E-08 5.8439458E-08 1,midg,midg; igrid,midg,midg 2.5535662E-08 9.7686383E-09 gauss-seidel spectral radius is 0.9889846 estimated iterations to convergence 78 setup time was (sec) 0.5300000 now iterating at: 14:06:05 rms-change max change #iterations 0.1913269 28.00828 at 10iterations 2.2268187E-02 3.796295 at 20iterations 2.7907502E-03 0.3933792 at 30iterations 4.6110051E-04 8.2033157E-02 at 40iterations 1.1601405E-04 1.8976212E-02 at 50iterations finished qdiffx linear iterations at : 14:06:08 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.1601405E-04 1.8976212E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:06:08 3.393u 0.138s 0:03.86 91.1% 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 Sun Oct 9 2011 at 14:06:08 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2387 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.060145 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): 21.44000 70.61600 ymin,ymax (A): -1.765000 50.07600 zmin,zma (A): -5.665000 37.15800 x,y,z range (A): 49.17599 51.84100 42.82300 scale (grids/A): 2.060145 object centre (A): 46.02800 24.15550 15.74650 number of atom coordinates read : 2387 total number of charged atoms : 2241 net assigned charge : 3.406023 assigned positive charge : 366.6511 centred at (gu) : 91.09296 87.15224 87.31319 assigned negative charge : -363.2455 centred at (gu) : 91.17028 86.70518 87.04572 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81040 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 30626 mr = 56631 m= 5383 mr = 23017 m= 472 mr = 3398 m= 10 mr = 209 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1495 time to turn everything in is 0.6000000 number of dielectric boundary points 34274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 17773 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) : 0.6867151 object centre at (A) : 46.02800 24.15550 15.74650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5708764E-03 4.8207901E-02 midg,1,midg; midg,igrid,midg -4.2343035E-02 1.0617062E-02 1,midg,midg; igrid,midg,midg 3.3303980E-02 -1.4427884E-02 gauss-seidel spectral radius is 0.9988050 estimated iterations to convergence 229 setup time was (sec) 0.8900000 now iterating at: 14:06:09 rms-change max change #iterations 4.775063 213.2054 at 10iterations 2.340639 80.09177 at 20iterations 1.148553 32.46264 at 30iterations 0.5673530 17.37502 at 40iterations 0.2792358 9.510649 at 50iterations 0.1373505 4.116103 at 60iterations 6.7709997E-02 2.004552 at 70iterations 3.3454888E-02 0.9874883 at 80iterations 1.6384156E-02 0.4619370 at 90iterations 8.1540709E-03 0.2466707 at 100iterations 4.0419707E-03 0.1235809 at 110iterations 2.0249276E-03 6.0874939E-02 at 120iterations finished qdiffx linear iterations at : 14:06:16 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 2.0249276E-03 6.0874939E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 14:06:17 7.735u 0.175s 0:08.20 96.3% 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 Sun Oct 9 2011 at 14:06:17 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2387 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.090218 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): 21.44000 70.61600 ymin,ymax (A): -1.765000 50.07600 zmin,zma (A): -5.665000 37.15800 x,y,z range (A): 49.17599 51.84100 42.82300 scale (grids/A): 3.090218 object centre (A): 46.02800 24.15550 15.74650 number of atom coordinates read : 2387 total number of charged atoms : 2241 net assigned charge : 3.406023 assigned positive charge : 366.6511 centred at (gu) : 91.63929 85.72815 85.96967 assigned negative charge : -363.2455 centred at (gu) : 91.75532 85.05775 85.56853 start vw surface at 0.1400000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 187006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 97382 mr = 136846 m= 37147 mr = 80463 m= 9858 mr = 30162 m= 1825 mr = 7373 m= 207 mr = 1244 m= 8 mr = 140 m= 0 mr = 4 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 5310 time to turn everything in is 1.900000 number of dielectric boundary points 77201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 17928 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) : 2.060145 object centre at (A) : 46.02800 24.15550 15.74650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8368789E-02 0.4333369 midg,1,midg; midg,igrid,midg -0.4377342 0.3220232 1,midg,midg; igrid,midg,midg 0.3585331 -0.4080021 gauss-seidel spectral radius is 0.9992911 estimated iterations to convergence 296 setup time was (sec) 2.210000 now iterating at: 14:06:19 rms-change max change #iterations 10.80490 419.9888 at 10iterations 6.357572 129.9352 at 20iterations 3.740877 68.05396 at 30iterations 2.197190 46.48660 at 40iterations 1.289340 24.70630 at 50iterations 0.7548802 12.80436 at 60iterations 0.4414164 7.863183 at 70iterations 0.2578218 4.396970 at 80iterations 0.1504542 2.629356 at 90iterations 8.7965392E-02 1.548481 at 100iterations 5.1177729E-02 0.9111252 at 110iterations 2.9898811E-02 0.4997826 at 120iterations 1.7459989E-02 0.3106241 at 130iterations 1.0228263E-02 0.1722747 at 140iterations 5.9991134E-03 0.1047897 at 150iterations 3.5557079E-03 6.7903519E-02 at 160iterations 2.1295347E-03 3.8406372E-02 at 170iterations 1.3041613E-03 2.4143219E-02 at 180iterations finished qdiffx linear iterations at : 14:06:30 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 1.3041613E-03 2.4143219E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 14:06:30 12.963u 0.177s 0:13.41 97.9% 0+0k 0+0io 0pf+0w