Wed Dec 21 14:21:53 PST 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 Wed Dec 21 2011 at 14:21:58 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! WARNING: PHE 153 has a net charge of -0.0320 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: 0.6404030 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): -5.187000 35.04600 ymin,ymax (A): -3.634000 49.36100 zmin,zma (A): -24.41400 31.17600 x,y,z range (A): 40.23300 52.99500 55.59000 scale (grids/A): 0.6404030 object centre (A): 14.92950 22.86350 3.381001 number of atom coordinates read : 1957 total number of charged atoms : 1825 net assigned charge : 1.968007 assigned positive charge : 291.3690 centred at (gu) : 90.59215 92.27456 90.13803 assigned negative charge : -289.4012 centred at (gu) : 90.71753 92.41647 90.08967 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5530 nv = 96 ne = 84 npr = 40034 no. pairs analyzed = 40034 no. exposed pairs = 2444 no. arc points = 17325 no. surface atoms = 825 nbur = 1132 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 286 mr = 3109 m= 0 mr = 34 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.1800000 number of dielectric boundary points 2673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1719 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2965441E-10 7.7078930E-09 midg,1,midg; midg,igrid,midg 9.5436921E-09 -1.5530764E-08 1,midg,midg; igrid,midg,midg 1.2401475E-08 -8.9237302E-09 gauss-seidel spectral radius is 0.9873105 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 14:21:59 rms-change max change #iterations 0.1273261 19.46573 at 10iterations 1.2599107E-02 2.363747 at 20iterations 1.2635572E-03 0.2016716 at 30iterations 1.2268100E-04 1.8610001E-02 at 40iterations 1.2164513E-05 1.8138885E-03 at 50iterations finished qdiffx linear iterations at : 14:22:02 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.2164513E-05 1.8138885E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 14:22:14 3.483u 0.215s 0:17.30 21.3% 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 Wed Dec 21 2011 at 14:22:17 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! WARNING: PHE 153 has a net charge of -0.0320 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: 1.921209 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): -5.187000 35.04600 ymin,ymax (A): -3.634000 49.36100 zmin,zma (A): -24.41400 31.17600 x,y,z range (A): 40.23300 52.99500 55.59000 scale (grids/A): 1.921209 object centre (A): 14.92950 22.86350 3.381001 number of atom coordinates read : 1957 total number of charged atoms : 1825 net assigned charge : 1.968007 assigned positive charge : 291.3690 centred at (gu) : 91.77661 96.82369 90.41391 assigned negative charge : -289.4012 centred at (gu) : 92.15267 97.24948 90.26913 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17325 grid for indexing accessible points = 1.400000 m= 22267 mr = 41180 m= 3478 mr = 17132 m= 157 mr = 2341 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 24589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14412 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) : 0.6404030 object centre at (A) : 14.92950 22.86350 3.381001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0990114E-02 8.0265924E-03 midg,1,midg; midg,igrid,midg 3.2194898E-02 -1.2146925E-02 1,midg,midg; igrid,midg,midg 9.1247112E-03 -6.3060638E-03 gauss-seidel spectral radius is 0.9985799 estimated iterations to convergence 210 setup time was (sec) 0.5600000 now iterating at: 14:22:21 rms-change max change #iterations 3.680523 168.1690 at 10iterations 1.699042 61.38734 at 20iterations 0.7874891 27.89461 at 30iterations 0.3643064 13.89849 at 40iterations 0.1666230 5.918608 at 50iterations 7.7009961E-02 2.797617 at 60iterations 3.5390083E-02 1.203497 at 70iterations 1.6376693E-02 0.5230219 at 80iterations 7.5545283E-03 0.2620201 at 90iterations 3.4809997E-03 0.1406851 at 100iterations 1.6146845E-03 6.2805176E-02 at 110iterations 7.4095069E-04 2.9559255E-02 at 120iterations finished qdiffx linear iterations at : 14:22:29 total time elapsed so far: 8.990000 # loops : 120 mean,max change (kT/e) : 7.4095069E-04 2.9559255E-02 energy calculations done at 8.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.120000 DelPhi exited at 14:22:39 9.121u 0.305s 0:23.07 40.8% 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 Wed Dec 21 2011 at 14:22:43 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! WARNING: PHE 153 has a net charge of -0.0320 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: 2.881813 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): -5.187000 35.04600 ymin,ymax (A): -3.634000 49.36100 zmin,zma (A): -24.41400 31.17600 x,y,z range (A): 40.23300 52.99500 55.59000 scale (grids/A): 2.881813 object centre (A): 14.92950 22.86350 3.381001 number of atom coordinates read : 1957 total number of charged atoms : 1825 net assigned charge : 1.968007 assigned positive charge : 291.3690 centred at (gu) : 92.66489 100.2355 90.62091 assigned negative charge : -289.4012 centred at (gu) : 93.22897 100.8744 90.40362 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 136999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17325 grid for indexing accessible points = 1.400000 m= 71203 mr = 99313 m= 27006 mr = 59396 m= 6394 mr = 22594 m= 758 mr = 5052 m= 32 mr = 481 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 55539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 14599 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) : 1.921209 object centre at (A) : 14.92950 22.86350 3.381001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.014790 -1.2399977E-02 midg,1,midg; midg,igrid,midg 0.3390439 -0.1591513 1,midg,midg; igrid,midg,midg 5.7526909E-02 -4.2709902E-02 gauss-seidel spectral radius is 0.9992302 estimated iterations to convergence 285 setup time was (sec) 1.030000 now iterating at: 14:22:49 rms-change max change #iterations 8.645662 422.5769 at 10iterations 4.955527 106.8714 at 20iterations 2.819354 59.27168 at 30iterations 1.603875 36.30366 at 40iterations 0.9118993 20.28033 at 50iterations 0.5168260 11.71058 at 60iterations 0.2931329 6.520676 at 70iterations 0.1663290 3.338624 at 80iterations 9.4125852E-02 1.810060 at 90iterations 5.3399142E-02 1.064941 at 100iterations 3.0221576E-02 0.6009636 at 110iterations 1.7155265E-02 0.3585939 at 120iterations 9.7345291E-03 0.1981828 at 130iterations 5.5124355E-03 0.1090126 at 140iterations 3.1265114E-03 5.8745384E-02 at 150iterations 1.7752445E-03 3.7322998E-02 at 160iterations 1.0040191E-03 1.8692017E-02 at 170iterations 5.6939822E-04 1.1558533E-02 at 180iterations finished qdiffx linear iterations at : 14:23:05 total time elapsed so far: 17.08000 # loops : 180 mean,max change (kT/e) : 5.6939822E-04 1.1558533E-02 energy calculations done at 17.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.21000 DelPhi exited at 14:23:08 17.214u 0.301s 0:24.78 70.6% 0+0k 0+0io 0pf+0w