Tue Oct 11 03:26:32 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 Tue Oct 11 2011 at 03:26:32 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 = 2558 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5931949 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): -16.00200 38.46200 ymin,ymax (A): 6.685000 55.39000 zmin,zma (A): 5.664000 65.67800 x,y,z range (A): 54.46400 48.70500 60.01400 scale (grids/A): 0.5931949 object centre (A): 11.23000 31.03750 35.67100 number of atom coordinates read : 2558 total number of charged atoms : 2409 net assigned charge : 8.8512897E-06 assigned positive charge : 382.7718 centred at (gu) : 89.08936 90.09836 90.24303 assigned negative charge : -382.7726 centred at (gu) : 89.02829 90.03063 90.34063 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6119 nv = 96 ne = 84 npr = 49348 no. pairs analyzed = 49348 no. exposed pairs = 3525 no. arc points = 25713 no. surface atoms = 1180 nbur = 1378 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 285 mr = 3021 m= 0 mr = 20 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.1900000 number of dielectric boundary points 3363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2606 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6749158E-09 -3.0093765E-09 midg,1,midg; midg,igrid,midg -1.9131323E-09 2.0252211E-09 1,midg,midg; igrid,midg,midg -2.1818110E-09 1.4476796E-09 gauss-seidel spectral radius is 0.9853028 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 03:26:32 rms-change max change #iterations 9.8282441E-02 18.41723 at 10iterations 8.1406143E-03 1.256239 at 20iterations 7.4138877E-04 0.1258011 at 30iterations 1.2523579E-04 2.7108192E-02 at 40iterations 3.7422349E-05 8.7680817E-03 at 50iterations finished qdiffx linear iterations at : 03:26:35 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 3.7422349E-05 8.7680817E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 03:26:36 3.417u 0.187s 0:04.15 86.5% 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 Tue Oct 11 2011 at 03:26:36 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 = 2558 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.779585 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): -16.00200 38.46200 ymin,ymax (A): 6.685000 55.39000 zmin,zma (A): 5.664000 65.67800 x,y,z range (A): 54.46400 48.70500 60.01400 scale (grids/A): 1.779585 object centre (A): 11.23000 31.03750 35.67100 number of atom coordinates read : 2558 total number of charged atoms : 2409 net assigned charge : 8.8512897E-06 assigned positive charge : 382.7718 centred at (gu) : 87.26746 90.29438 90.72823 assigned negative charge : -382.7726 centred at (gu) : 87.08469 90.09172 91.02171 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66764 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25713 grid for indexing accessible points = 1.400000 m= 21223 mr = 43771 m= 2504 mr = 14394 m= 92 mr = 1271 m= 0 mr = 25 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 527 time to turn everything in is 0.3400000 number of dielectric boundary points 31122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 18777 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) : 0.5931949 object centre at (A) : 11.23000 31.03750 35.67100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1667569E-02 -1.7693559E-02 midg,1,midg; midg,igrid,midg -1.5068920E-02 9.2317071E-03 1,midg,midg; igrid,midg,midg -8.6534228E-03 3.3413467E-04 gauss-seidel spectral radius is 0.9984512 estimated iterations to convergence 202 setup time was (sec) 0.6000000 now iterating at: 03:26:37 rms-change max change #iterations 3.675176 167.9744 at 10iterations 1.624862 71.98019 at 20iterations 0.7227146 28.05189 at 30iterations 0.3208745 11.93903 at 40iterations 0.1425644 5.073117 at 50iterations 6.3562781E-02 2.306539 at 60iterations 2.8307933E-02 0.9669228 at 70iterations 1.2666460E-02 0.4672623 at 80iterations 5.6456984E-03 0.1997375 at 90iterations 2.5225498E-03 9.4261169E-02 at 100iterations 1.1335220E-03 4.1976929E-02 at 110iterations 5.1982631E-04 1.8286228E-02 at 120iterations finished qdiffx linear iterations at : 03:26:45 total time elapsed so far: 8.580000 # loops : 120 mean,max change (kT/e) : 5.1982631E-04 1.8286228E-02 energy calculations done at 8.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.710000 DelPhi exited at 03:26:46 8.711u 0.308s 0:09.51 94.7% 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 Tue Oct 11 2011 at 03:26:46 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 = 2558 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.669377 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): -16.00200 38.46200 ymin,ymax (A): 6.685000 55.39000 zmin,zma (A): 5.664000 65.67800 x,y,z range (A): 54.46400 48.70500 60.01400 scale (grids/A): 2.669377 object centre (A): 11.23000 31.03750 35.67100 number of atom coordinates read : 2558 total number of charged atoms : 2409 net assigned charge : 8.8512897E-06 assigned positive charge : 382.7718 centred at (gu) : 85.90110 90.44150 91.09216 assigned negative charge : -382.7726 centred at (gu) : 85.62699 90.13756 91.53246 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 154533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25713 grid for indexing accessible points = 1.400000 m= 71676 mr = 106856 m= 21783 mr = 56319 m= 4129 mr = 16193 m= 399 mr = 2745 m= 21 mr = 213 m= 0 mr = 4 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1846 time to turn everything in is 0.8700000 number of dielectric boundary points 70211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 19266 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) : 1.779585 object centre at (A) : 11.23000 31.03750 35.67100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1809638 -0.1589142 midg,1,midg; midg,igrid,midg -0.2354747 0.1326247 1,midg,midg; igrid,midg,midg -0.1329074 -1.9116268E-02 gauss-seidel spectral radius is 0.9992173 estimated iterations to convergence 282 setup time was (sec) 1.170000 now iterating at: 03:26:47 rms-change max change #iterations 9.163230 341.3882 at 10iterations 5.350606 171.4805 at 20iterations 3.091554 73.36685 at 30iterations 1.778774 40.63769 at 40iterations 1.018544 23.32589 at 50iterations 0.5821760 14.44508 at 60iterations 0.3316821 7.874600 at 70iterations 0.1891181 4.536538 at 80iterations 0.1071821 2.216982 at 90iterations 6.0896657E-02 1.324145 at 100iterations 3.4549784E-02 0.7233832 at 110iterations 1.9618217E-02 0.3881474 at 120iterations 1.1104985E-02 0.2208776 at 130iterations 6.2771291E-03 0.1264496 at 140iterations 3.5626381E-03 7.4414253E-02 at 150iterations 2.0154801E-03 4.2446136E-02 at 160iterations 1.1398939E-03 2.1559715E-02 at 170iterations 6.4464286E-04 1.2549162E-02 at 180iterations finished qdiffx linear iterations at : 03:26:59 total time elapsed so far: 13.40000 # loops : 180 mean,max change (kT/e) : 6.4464286E-04 1.2549162E-02 energy calculations done at 13.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 03:27:00 13.530u 0.299s 0:14.14 97.7% 0+0k 0+0io 0pf+0w