Mon Oct 10 13:54:52 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 Mon Oct 10 2011 at 13:54:52 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4996 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5549666 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): 3.189000 65.00800 ymin,ymax (A): -8.794000 53.52900 zmin,zma (A): -2.167000 61.98100 x,y,z range (A): 61.81900 62.32300 64.14800 scale (grids/A): 0.5549666 object centre (A): 34.09850 22.36750 29.90700 number of atom coordinates read : 4996 total number of charged atoms : 4868 net assigned charge : 2.635039 assigned positive charge : 772.7608 centred at (gu) : 88.50356 89.19196 89.36998 assigned negative charge : -770.1316 centred at (gu) : 88.37764 89.21954 89.36966 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10060 nv = 96 ne = 84 npr = 100325 no. pairs analyzed = 100325 no. exposed pairs = 5832 no. arc points = 39191 no. surface atoms = 1986 nbur = 3010 mkacc time = 0.1700000 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 = 1.540000 m= 478 mr = 5778 m= 4 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4050 ## 436 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 13148 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9846836E-10 2.3001956E-10 midg,1,midg; midg,igrid,midg 8.5433738E-10 -1.4542556E-10 1,midg,midg; igrid,midg,midg -2.5953957E-09 1.5539691E-09 gauss-seidel spectral radius is 0.9834018 estimated iterations to convergence 64 setup time was (sec) 0.5200000 now iterating at: 13:54:53 rms-change max change #iterations 0.1108323 15.58948 at 10iterations 1.0339320E-02 1.469025 at 20iterations 3.0891362E-03 0.3154831 at 30iterations 1.4818235E-03 0.1581106 at 40iterations 7.3838298E-04 8.2746506E-02 at 50iterations finished qdiffx linear iterations at : 13:54:56 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 7.3838298E-04 8.2746506E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 13:54:56 3.543u 0.191s 0:04.40 84.7% 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 Mon Oct 10 2011 at 13:54:56 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4996 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.664900 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): 3.189000 65.00800 ymin,ymax (A): -8.794000 53.52900 zmin,zma (A): -2.167000 61.98100 x,y,z range (A): 61.81900 62.32300 64.14800 scale (grids/A): 1.664900 object centre (A): 34.09850 22.36750 29.90700 number of atom coordinates read : 4996 total number of charged atoms : 4868 net assigned charge : 2.635039 assigned positive charge : 772.7608 centred at (gu) : 85.50935 87.57426 88.10825 assigned negative charge : -770.1316 centred at (gu) : 85.13294 87.65878 88.10904 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 111895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39191 grid for indexing accessible points = 1.400000 m= 40014 mr = 81418 m= 4973 mr = 29181 m= 183 mr = 2722 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 188 time to turn everything in is 0.5500000 number of dielectric boundary points 43721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 371 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 37411 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) : 0.5549666 object centre at (A) : 34.09850 22.36750 29.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0707823E-02 -2.8546479E-02 midg,1,midg; midg,igrid,midg 2.2257738E-02 9.7186426E-03 1,midg,midg; igrid,midg,midg -2.0270066E-02 3.7016023E-02 gauss-seidel spectral radius is 0.9984419 estimated iterations to convergence 201 setup time was (sec) 0.7700000 now iterating at: 13:54:57 rms-change max change #iterations 4.837513 218.6949 at 10iterations 2.150900 64.97473 at 20iterations 0.9571395 27.06037 at 30iterations 0.4261411 11.34208 at 40iterations 0.1900670 5.230904 at 50iterations 8.5466951E-02 2.536594 at 60iterations 3.8921759E-02 1.054998 at 70iterations 1.8191081E-02 0.5227814 at 80iterations 9.2781167E-03 0.2636871 at 90iterations 5.4184338E-03 0.1578674 at 100iterations 3.6254986E-03 9.0896606E-02 at 110iterations 2.6666834E-03 6.2767029E-02 at 120iterations finished qdiffx linear iterations at : 13:55:05 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 2.6666834E-03 6.2767029E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 13:55:05 8.136u 0.190s 0:08.64 96.2% 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 Mon Oct 10 2011 at 13:55:09 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4996 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.497350 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): 3.189000 65.00800 ymin,ymax (A): -8.794000 53.52900 zmin,zma (A): -2.167000 61.98100 x,y,z range (A): 61.81900 62.32300 64.14800 scale (grids/A): 2.497350 object centre (A): 34.09850 22.36750 29.90700 number of atom coordinates read : 4996 total number of charged atoms : 4868 net assigned charge : 2.635039 assigned positive charge : 772.7608 centred at (gu) : 83.26366 86.36117 87.16202 assigned negative charge : -770.1316 centred at (gu) : 82.69937 86.48810 87.16349 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 259983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39191 grid for indexing accessible points = 1.400000 m= 133212 mr = 197600 m= 43802 mr = 109140 m= 8222 mr = 34463 m= 745 mr = 5689 m= 19 mr = 396 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 722 time to turn everything in is 1.380000 number of dielectric boundary points 98695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 38919 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) : 1.664900 object centre at (A) : 34.09850 22.36750 29.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3610292 -0.6655370 midg,1,midg; midg,igrid,midg 8.5720755E-02 -1.3961109E-03 1,midg,midg; igrid,midg,midg -0.4098502 0.5182815 gauss-seidel spectral radius is 0.9992563 estimated iterations to convergence 289 setup time was (sec) 1.630000 now iterating at: 13:55:11 rms-change max change #iterations 12.25761 338.9139 at 10iterations 7.238661 166.4363 at 20iterations 4.246641 79.29560 at 30iterations 2.482741 48.96321 at 40iterations 1.446468 25.66296 at 50iterations 0.8389000 14.57584 at 60iterations 0.4861841 8.382877 at 70iterations 0.2815438 5.052570 at 80iterations 0.1630659 2.664340 at 90iterations 9.4205230E-02 1.520384 at 100iterations 5.4652520E-02 0.9495115 at 110iterations 3.1859986E-02 0.4923234 at 120iterations 1.8785439E-02 0.2962418 at 130iterations 1.1358642E-02 0.1827221 at 140iterations 7.1783438E-03 0.1178379 at 150iterations 4.8401603E-03 8.2229614E-02 at 160iterations 3.5301223E-03 5.7186127E-02 at 170iterations 2.7490833E-03 4.1740417E-02 at 180iterations finished qdiffx linear iterations at : 13:55:23 total time elapsed so far: 13.50000 # loops : 180 mean,max change (kT/e) : 2.7490833E-03 4.1740417E-02 energy calculations done at 13.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.64000 DelPhi exited at 13:55:24 13.640u 0.198s 0:14.32 96.5% 0+0k 0+0io 0pf+0w