Sat Oct 8 21:15:52 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 Sat Oct 8 2011 at 21:15:52 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 546 has a net charge of 1.4000 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: 0.6216603 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): -31.96200 17.30700 ymin,ymax (A): -23.54400 23.41800 zmin,zma (A): -12.42300 44.84300 x,y,z range (A): 49.26900 46.96200 57.26600 scale (grids/A): 0.6216603 object centre (A): -7.327500 -6.2999725E-02 16.21000 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 88.63430 88.97179 89.63908 assigned negative charge : -389.0045 centred at (gu) : 88.55174 89.02656 89.51934 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6475 nv = 96 ne = 84 npr = 54009 no. pairs analyzed = 54009 no. exposed pairs = 3016 no. arc points = 21242 no. surface atoms = 1006 nbur = 1583 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3652 m= 0 mr = 26 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 0.3400000 number of dielectric boundary points 3122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2147 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8155 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4298659E-09 1.0803570E-08 midg,1,midg; midg,igrid,midg 9.0981738E-09 -2.6618324E-10 1,midg,midg; igrid,midg,midg -3.2645957E-09 6.8058879E-09 gauss-seidel spectral radius is 0.9865935 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 21:15:53 rms-change max change #iterations 0.1272746 20.34919 at 10iterations 1.2069892E-02 1.949080 at 20iterations 1.1021182E-03 0.1608429 at 30iterations 1.0381889E-04 1.7407894E-02 at 40iterations 9.6149834E-06 1.3427734E-03 at 50iterations finished qdiffx linear iterations at : 21:15:56 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 9.6149834E-06 1.3427734E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 21:15:57 4.044u 0.271s 0:04.58 94.1% 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 Sat Oct 8 2011 at 21:15:57 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 546 has a net charge of 1.4000 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: 1.864981 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): -31.96200 17.30700 ymin,ymax (A): -23.54400 23.41800 zmin,zma (A): -12.42300 44.84300 x,y,z range (A): 49.26900 46.96200 57.26600 scale (grids/A): 1.864981 object centre (A): -7.327500 -6.2999725E-02 16.21000 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 85.90248 86.91515 88.91707 assigned negative charge : -389.0045 centred at (gu) : 85.65462 87.07949 88.55808 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 71088 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21242 grid for indexing accessible points = 1.400000 m= 24110 mr = 50053 m= 3300 mr = 17735 m= 165 mr = 2007 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 5527 time to turn everything in is 0.6200000 number of dielectric boundary points 28822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19278 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) : 0.6216603 object centre at (A) : -7.327500 -6.2999725E-02 16.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2884307E-02 1.8191913E-02 midg,1,midg; midg,igrid,midg 1.6203064E-02 5.0600450E-03 1,midg,midg; igrid,midg,midg -3.4027460E-03 2.8406791E-02 gauss-seidel spectral radius is 0.9985723 estimated iterations to convergence 210 setup time was (sec) 0.9200000 now iterating at: 21:15:58 rms-change max change #iterations 4.070558 193.4707 at 10iterations 1.873383 68.36868 at 20iterations 0.8602151 27.41614 at 30iterations 0.3954026 12.26741 at 40iterations 0.1835133 6.781857 at 50iterations 8.3996505E-02 2.674484 at 60iterations 3.8785513E-02 1.298286 at 70iterations 1.7840823E-02 0.5717640 at 80iterations 8.2059503E-03 0.2706757 at 90iterations 3.7890852E-03 0.1169891 at 100iterations 1.7436286E-03 5.4409027E-02 at 110iterations 8.0493430E-04 2.4364471E-02 at 120iterations finished qdiffx linear iterations at : 21:16:06 total time elapsed so far: 9.120000 # loops : 120 mean,max change (kT/e) : 8.0493430E-04 2.4364471E-02 energy calculations done at 9.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.300000 DelPhi exited at 21:16:07 9.305u 0.289s 0:09.85 97.2% 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 Sat Oct 8 2011 at 21:16:07 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 546 has a net charge of 1.4000 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: 2.797471 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): -31.96200 17.30700 ymin,ymax (A): -23.54400 23.41800 zmin,zma (A): -12.42300 44.84300 x,y,z range (A): 49.26900 46.96200 57.26600 scale (grids/A): 2.797471 object centre (A): -7.327500 -6.2999725E-02 16.21000 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 83.85359 85.37254 88.37538 assigned negative charge : -389.0045 centred at (gu) : 83.48196 85.61928 87.83696 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 164772 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21242 grid for indexing accessible points = 1.400000 m= 80701 mr = 121019 m= 26562 mr = 66480 m= 5793 mr = 21274 m= 654 mr = 4311 m= 24 mr = 399 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 19198 time to turn everything in is 1.560000 number of dielectric boundary points 65014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 19629 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) : 1.864981 object centre at (A) : -7.327500 -6.2999725E-02 16.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1710250 0.1809076 midg,1,midg; midg,igrid,midg 0.1788309 4.1632295E-02 1,midg,midg; igrid,midg,midg -1.7580722E-02 0.3459277 gauss-seidel spectral radius is 0.9992337 estimated iterations to convergence 285 setup time was (sec) 1.870000 now iterating at: 21:16:09 rms-change max change #iterations 9.490514 366.3984 at 10iterations 5.444469 144.6132 at 20iterations 3.109586 82.51369 at 30iterations 1.770386 40.22945 at 40iterations 1.009655 23.18869 at 50iterations 0.5734087 10.66645 at 60iterations 0.3267741 5.994102 at 70iterations 0.1855404 3.464993 at 80iterations 0.1058327 1.930875 at 90iterations 5.9923332E-02 1.304225 at 100iterations 3.4151182E-02 0.6745310 at 110iterations 1.9441061E-02 0.3707991 at 120iterations 1.1050864E-02 0.2319126 at 130iterations 6.2829535E-03 0.1304417 at 140iterations 3.5720996E-03 6.6108704E-02 at 150iterations 2.0240496E-03 3.7784815E-02 at 160iterations 1.1548471E-03 2.3349762E-02 at 170iterations 6.5417506E-04 1.3526917E-02 at 180iterations finished qdiffx linear iterations at : 21:16:22 total time elapsed so far: 15.27000 # loops : 180 mean,max change (kT/e) : 6.5417506E-04 1.3526917E-02 energy calculations done at 15.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.46000 DelPhi exited at 21:16:23 15.458u 0.304s 0:16.03 98.2% 0+0k 0+0io 0pf+0w