Sat Oct 8 14:06:35 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 Sat Oct 8 2011 at 14:06:35 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2979 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6568508 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): -11.98300 42.21500 ymin,ymax (A): -23.03400 22.57800 zmin,zma (A): -6.174000 46.96000 x,y,z range (A): 54.19800 45.61200 53.13400 scale (grids/A): 0.6568508 object centre (A): 15.11600 -0.2280006 20.39300 number of atom coordinates read : 2979 total number of charged atoms : 2832 net assigned charge : -1.999991 assigned positive charge : 445.8266 centred at (gu) : 89.04131 89.70931 91.30648 assigned negative charge : -447.8274 centred at (gu) : 89.04740 89.60616 91.27258 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8604 nv = 96 ne = 84 npr = 62447 no. pairs analyzed = 62447 no. exposed pairs = 3401 no. arc points = 23564 no. surface atoms = 1155 nbur = 1824 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 479 mr = 5103 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2224 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 10293 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0303516E-09 3.2773788E-09 midg,1,midg; midg,igrid,midg -2.8282535E-08 1.5717422E-08 1,midg,midg; igrid,midg,midg -4.1275450E-09 -4.9146900E-09 gauss-seidel spectral radius is 0.9880155 estimated iterations to convergence 75 setup time was (sec) 0.4400000 now iterating at: 14:06:36 rms-change max change #iterations 0.1799374 25.36579 at 10iterations 1.9476591E-02 2.358429 at 20iterations 2.1058391E-03 0.2674599 at 30iterations 2.5927837E-04 2.8541565E-02 at 40iterations 3.7000817E-05 4.3945313E-03 at 50iterations finished qdiffx linear iterations at : 14:06:39 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 3.7000817E-05 4.3945313E-03 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 14:06:39 3.761u 0.225s 0:04.31 92.3% 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 Sat Oct 8 2011 at 14:06:39 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2979 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.970552 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): -11.98300 42.21500 ymin,ymax (A): -23.03400 22.57800 zmin,zma (A): -6.174000 46.96000 x,y,z range (A): 54.19800 45.61200 53.13400 scale (grids/A): 1.970552 object centre (A): 15.11600 -0.2280006 20.39300 number of atom coordinates read : 2979 total number of charged atoms : 2832 net assigned charge : -1.999991 assigned positive charge : 445.8266 centred at (gu) : 87.12326 89.12730 93.91919 assigned negative charge : -447.8274 centred at (gu) : 87.14205 88.81828 93.81744 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 93093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23564 grid for indexing accessible points = 1.400000 m= 34810 mr = 67706 m= 5658 mr = 26352 m= 378 mr = 3571 m= 6 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 193 time to turn everything in is 0.4800000 number of dielectric boundary points 36196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 22378 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) : 0.6568508 object centre at (A) : 15.11600 -0.2280006 20.39300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5154334E-02 1.4369115E-02 midg,1,midg; midg,igrid,midg -6.5936660E-03 1.8962365E-02 1,midg,midg; igrid,midg,midg -4.2823639E-02 -7.7795866E-03 gauss-seidel spectral radius is 0.9987504 estimated iterations to convergence 224 setup time was (sec) 0.7800000 now iterating at: 14:06:40 rms-change max change #iterations 4.962108 205.5139 at 10iterations 2.414118 70.11963 at 20iterations 1.167576 33.13263 at 30iterations 0.5667585 17.26366 at 40iterations 0.2754530 7.278345 at 50iterations 0.1333719 3.959661 at 60iterations 6.4630762E-02 2.040252 at 70iterations 3.1276468E-02 0.9286041 at 80iterations 1.5255953E-02 0.4033337 at 90iterations 7.3645720E-03 0.2045891 at 100iterations 3.5870273E-03 9.2145920E-02 at 110iterations 1.7397839E-03 4.5536041E-02 at 120iterations finished qdiffx linear iterations at : 14:06:49 total time elapsed so far: 9.750000 # loops : 120 mean,max change (kT/e) : 1.7397839E-03 4.5536041E-02 energy calculations done at 9.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.880000 DelPhi exited at 14:06:50 9.882u 0.323s 0:10.63 95.9% 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 14:06:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2979 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.955829 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): -11.98300 42.21500 ymin,ymax (A): -23.03400 22.57800 zmin,zma (A): -6.174000 46.96000 x,y,z range (A): 54.19800 45.61200 53.13400 scale (grids/A): 2.955829 object centre (A): 15.11600 -0.2280006 20.39300 number of atom coordinates read : 2979 total number of charged atoms : 2832 net assigned charge : -1.999991 assigned positive charge : 445.8266 centred at (gu) : 85.68468 88.69087 95.87862 assigned negative charge : -447.8274 centred at (gu) : 85.71307 88.22743 95.72597 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 215650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23564 grid for indexing accessible points = 1.400000 m= 112662 mr = 163449 m= 41364 mr = 94262 m= 10264 mr = 33661 m= 1558 mr = 7606 m= 91 mr = 995 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 616 time to turn everything in is 1.250000 number of dielectric boundary points 81589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 22656 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) : 1.970552 object centre at (A) : 15.11600 -0.2280006 20.39300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5035037E-02 0.4551605 midg,1,midg; midg,igrid,midg -4.4659831E-02 0.2089819 1,midg,midg; igrid,midg,midg -0.5185972 2.0212758E-02 gauss-seidel spectral radius is 0.9992918 estimated iterations to convergence 296 setup time was (sec) 1.560000 now iterating at: 14:06:52 rms-change max change #iterations 11.34082 395.3593 at 10iterations 6.682927 142.0229 at 20iterations 3.933642 82.18994 at 30iterations 2.308297 45.29377 at 40iterations 1.355218 23.70404 at 50iterations 0.7923984 12.63521 at 60iterations 0.4624529 8.210400 at 70iterations 0.2699638 4.134949 at 80iterations 0.1576855 2.591138 at 90iterations 9.2059731E-02 1.439642 at 100iterations 5.3706408E-02 0.8076782 at 110iterations 3.1323142E-02 0.4915848 at 120iterations 1.8228464E-02 0.3125610 at 130iterations 1.0652158E-02 0.1585376 at 140iterations 6.2401569E-03 9.7139120E-02 at 150iterations 3.6470110E-03 5.5768967E-02 at 160iterations 2.1486387E-03 3.4974158E-02 at 170iterations 1.2739961E-03 2.1217346E-02 at 180iterations finished qdiffx linear iterations at : 14:07:05 total time elapsed so far: 14.90000 # loops : 180 mean,max change (kT/e) : 1.2739961E-03 2.1217346E-02 energy calculations done at 14.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.03000 DelPhi exited at 14:07:06 15.030u 0.311s 0:15.61 98.2% 0+0k 0+0io 0pf+0w