Tue Nov 22 14:12:44 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 Tue Nov 22 2011 at 14:12:49 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 0.6320686 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): -35.11700 10.05800 ymin,ymax (A): 1.027000 42.85800 zmin,zma (A): -0.8770000 55.44600 x,y,z range (A): 45.17500 41.83100 56.32300 scale (grids/A): 0.6320686 object centre (A): -12.52950 21.94250 27.28450 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 289.2440 centred at (gu) : 90.41092 89.05651 90.35509 assigned negative charge : -286.2443 centred at (gu) : 90.34023 89.20385 90.39366 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5364 nv = 96 ne = 84 npr = 39572 no. pairs analyzed = 39572 no. exposed pairs = 2513 no. arc points = 17458 no. surface atoms = 854 nbur = 1088 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 2884 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1753 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6262 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5715428E-09 7.1849099E-10 midg,1,midg; midg,igrid,midg 1.6441255E-08 -5.6523137E-09 1,midg,midg; igrid,midg,midg -1.4160391E-09 8.9651913E-09 gauss-seidel spectral radius is 0.9869789 estimated iterations to convergence 72 setup time was (sec) 0.4500000 now iterating at: 14:12:52 rms-change max change #iterations 0.1227802 21.33231 at 10iterations 1.1645949E-02 1.787203 at 20iterations 1.0752033E-03 0.2035401 at 30iterations 1.0466909E-04 1.6765118E-02 at 40iterations 9.9378340E-06 1.7604828E-03 at 50iterations finished qdiffx linear iterations at : 14:13:01 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 9.9378340E-06 1.7604828E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 14:13:08 3.310u 0.179s 0:20.21 17.2% 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 Nov 22 2011 at 14:13:10 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 1.896206 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): -35.11700 10.05800 ymin,ymax (A): 1.027000 42.85800 zmin,zma (A): -0.8770000 55.44600 x,y,z range (A): 45.17500 41.83100 56.32300 scale (grids/A): 1.896206 object centre (A): -12.52950 21.94250 27.28450 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 289.2440 centred at (gu) : 91.23283 87.16953 91.06498 assigned negative charge : -286.2443 centred at (gu) : 91.02107 87.61172 91.18118 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 57072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17458 grid for indexing accessible points = 1.400000 m= 21535 mr = 38829 m= 3628 mr = 16000 m= 223 mr = 2351 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 312 time to turn everything in is 0.4600000 number of dielectric boundary points 25199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14236 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) : 0.6320686 object centre at (A) : -12.52950 21.94250 27.28450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4735102E-02 3.4546327E-02 midg,1,midg; midg,igrid,midg 6.9987755E-03 -7.6116663E-03 1,midg,midg; igrid,midg,midg -7.3668119E-03 -2.3005966E-03 gauss-seidel spectral radius is 0.9985492 estimated iterations to convergence 208 setup time was (sec) 0.7700000 now iterating at: 14:13:16 rms-change max change #iterations 3.568318 150.7322 at 10iterations 1.636575 65.64043 at 20iterations 0.7512320 26.86366 at 30iterations 0.3420957 12.50352 at 40iterations 0.1552018 5.515454 at 50iterations 7.1411207E-02 2.606182 at 60iterations 3.2594033E-02 1.344992 at 70iterations 1.4858862E-02 0.6821311 at 80iterations 6.8112849E-03 0.2335510 at 90iterations 3.1143080E-03 0.1122365 at 100iterations 1.4294569E-03 5.4317474E-02 at 110iterations 6.4845034E-04 2.2500277E-02 at 120iterations finished qdiffx linear iterations at : 14:13:37 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 6.4845034E-04 2.2500277E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 14:13:39 7.978u 0.230s 0:28.80 28.4% 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 Tue Nov 22 2011 at 14:13:42 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 2.844309 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): -35.11700 10.05800 ymin,ymax (A): 1.027000 42.85800 zmin,zma (A): -0.8770000 55.44600 x,y,z range (A): 45.17500 41.83100 56.32300 scale (grids/A): 2.844309 object centre (A): -12.52950 21.94250 27.28450 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 289.2440 centred at (gu) : 91.84923 85.75428 91.59749 assigned negative charge : -286.2443 centred at (gu) : 91.53162 86.41757 91.77177 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 131596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17458 grid for indexing accessible points = 1.400000 m= 67628 mr = 93819 m= 26348 mr = 55381 m= 6535 mr = 21534 m= 934 mr = 4989 m= 47 mr = 610 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 1077 time to turn everything in is 1.110000 number of dielectric boundary points 56739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 14478 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) : 1.896206 object centre at (A) : -12.52950 21.94250 27.28450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3362569E-02 0.2565464 midg,1,midg; midg,igrid,midg -1.8336695E-02 -9.5782071E-02 1,midg,midg; igrid,midg,midg -0.1061874 -6.8516903E-02 gauss-seidel spectral radius is 0.9992205 estimated iterations to convergence 283 setup time was (sec) 1.440000 now iterating at: 14:13:49 rms-change max change #iterations 8.457176 417.0481 at 10iterations 4.863053 135.2304 at 20iterations 2.767402 59.65667 at 30iterations 1.580288 34.66608 at 40iterations 0.8950154 20.70842 at 50iterations 0.5066379 10.32854 at 60iterations 0.2881279 5.983025 at 70iterations 0.1629884 3.232308 at 80iterations 9.2381127E-02 1.862141 at 90iterations 5.2257020E-02 1.030602 at 100iterations 2.9476155E-02 0.5880108 at 110iterations 1.6690698E-02 0.3766580 at 120iterations 9.4419532E-03 0.1824112 at 130iterations 5.3381883E-03 0.1160078 at 140iterations 3.0178970E-03 6.6431046E-02 at 150iterations 1.7054514E-03 3.2720327E-02 at 160iterations 9.6394191E-04 2.1415710E-02 at 170iterations 5.4546027E-04 1.0427237E-02 at 180iterations finished qdiffx linear iterations at : 14:14:21 total time elapsed so far: 11.91000 # loops : 180 mean,max change (kT/e) : 5.4546027E-04 1.0427237E-02 energy calculations done at 11.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 14:14:23 12.096u 0.197s 0:41.84 29.3% 0+0k 0+0io 0pf+0w