Tue Oct 11 03:20:17 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 Tue Oct 11 2011 at 03:20:17 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3508 !!! WARNING: GLM 19 has a net charge of -0.0940 !!! WARNING: SEP 84 has a net charge of -0.4750 !!! WARNING: GLM 135 has a net charge of -0.0940 !!! WARNING: GLU 167 has a net charge of -0.2720 !!! WARNING: SEP 229 has a net charge of -0.4750 !!! WARNING: SER 505 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5425341 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): -11.26100 42.94900 ymin,ymax (A): 14.38300 74.10800 zmin,zma (A): 36.81000 102.4280 x,y,z range (A): 54.21000 59.72500 65.61800 scale (grids/A): 0.5425341 object centre (A): 15.84400 44.24550 69.61900 number of atom coordinates read : 3508 total number of charged atoms : 3357 net assigned charge : -8.181977 assigned positive charge : 530.7753 centred at (gu) : 88.67163 87.73717 88.89568 assigned negative charge : -538.9588 centred at (gu) : 88.68665 87.74616 88.90821 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6632 nv = 96 ne = 84 npr = 70787 no. pairs analyzed = 70787 no. exposed pairs = 4444 no. arc points = 31536 no. surface atoms = 1475 nbur = 2033 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 = 1.568000 m= 281 mr = 3408 m= 0 mr = 9 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.4200000 number of dielectric boundary points 3496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3213 ## 413 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8806 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6551135E-10 -4.0768375E-10 midg,1,midg; midg,igrid,midg -6.6132655E-10 -2.9506325E-10 1,midg,midg; igrid,midg,midg -4.6700682E-10 -3.9888570E-10 gauss-seidel spectral radius is 0.9825265 estimated iterations to convergence 62 setup time was (sec) 0.6600000 now iterating at: 03:20:18 rms-change max change #iterations 8.0722049E-02 12.56411 at 10iterations 5.4507912E-03 0.8996887 at 20iterations 6.0222793E-04 7.8243256E-02 at 30iterations 1.3628039E-04 1.9255221E-02 at 40iterations 3.6586851E-05 5.3751469E-03 at 50iterations finished qdiffx linear iterations at : 03:20:21 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 3.6586851E-05 5.3751469E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 03:20:22 3.714u 0.228s 0:04.46 88.1% 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 Tue Oct 11 2011 at 03:20:22 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3508 !!! WARNING: GLM 19 has a net charge of -0.0940 !!! WARNING: SEP 84 has a net charge of -0.4750 !!! WARNING: GLM 135 has a net charge of -0.0940 !!! WARNING: GLU 167 has a net charge of -0.2720 !!! WARNING: SEP 229 has a net charge of -0.4750 !!! WARNING: SER 505 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.627602 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): -11.26100 42.94900 ymin,ymax (A): 14.38300 74.10800 zmin,zma (A): 36.81000 102.4280 x,y,z range (A): 54.21000 59.72500 65.61800 scale (grids/A): 1.627602 object centre (A): 15.84400 44.24550 69.61900 number of atom coordinates read : 3508 total number of charged atoms : 3357 net assigned charge : -8.181977 assigned positive charge : 530.7753 centred at (gu) : 86.01385 83.21062 86.68585 assigned negative charge : -538.9588 centred at (gu) : 86.05936 83.23804 86.72433 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73939 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22402 mr = 50088 m= 2264 mr = 15147 m= 51 mr = 1053 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1009 time to turn everything in is 0.5900000 number of dielectric boundary points 32369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 434 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 25682 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) : 0.5425341 object centre at (A) : 15.84400 44.24550 69.61900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8167068E-03 1.6121026E-02 midg,1,midg; midg,igrid,midg -2.5401243E-03 -4.3746755E-03 1,midg,midg; igrid,midg,midg -3.5613934E-03 -1.8399232E-03 gauss-seidel spectral radius is 0.9982234 estimated iterations to convergence 188 setup time was (sec) 0.9000000 now iterating at: 03:20:23 rms-change max change #iterations 3.656036 185.0218 at 10iterations 1.533460 50.90814 at 20iterations 0.6463851 21.52731 at 30iterations 0.2708587 9.410553 at 40iterations 0.1140341 3.750023 at 50iterations 4.8007611E-02 1.587527 at 60iterations 2.0245019E-02 0.7440529 at 70iterations 8.5892882E-03 0.2802383 at 80iterations 3.6719779E-03 0.1268153 at 90iterations 1.5957045E-03 5.3482533E-02 at 100iterations 7.0860604E-04 2.5138855E-02 at 110iterations 3.3132525E-04 1.1927128E-02 at 120iterations finished qdiffx linear iterations at : 03:20:31 total time elapsed so far: 8.780000 # loops : 120 mean,max change (kT/e) : 3.3132525E-04 1.1927128E-02 energy calculations done at 8.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.970000 DelPhi exited at 03:20:31 8.970u 0.265s 0:09.77 94.4% 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 Oct 11 2011 at 03:20:31 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3508 !!! WARNING: GLM 19 has a net charge of -0.0940 !!! WARNING: SEP 84 has a net charge of -0.4750 !!! WARNING: GLM 135 has a net charge of -0.0940 !!! WARNING: GLU 167 has a net charge of -0.2720 !!! WARNING: SEP 229 has a net charge of -0.4750 !!! WARNING: SER 505 has a net charge of -0.2720 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: 2.441403 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): -11.26100 42.94900 ymin,ymax (A): 14.38300 74.10800 zmin,zma (A): 36.81000 102.4280 x,y,z range (A): 54.21000 59.72500 65.61800 scale (grids/A): 2.441403 object centre (A): 15.84400 44.24550 69.61900 number of atom coordinates read : 3508 total number of charged atoms : 3357 net assigned charge : -8.181977 assigned positive charge : 530.7753 centred at (gu) : 84.02052 79.81573 85.02861 assigned negative charge : -538.9588 centred at (gu) : 84.08904 79.85705 85.08640 start vw surface at 0.1700000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 171711 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 78146 mr = 122487 m= 21823 mr = 61425 m= 3473 mr = 16158 m= 216 mr = 2187 m= 2 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 3163 time to turn everything in is 1.350000 number of dielectric boundary points 73034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 26819 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) : 1.627602 object centre at (A) : 15.84400 44.24550 69.61900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1942443 0.3959286 midg,1,midg; midg,igrid,midg 1.8638914E-02 3.1005659E-03 1,midg,midg; igrid,midg,midg -1.6885206E-02 -4.6024118E-02 gauss-seidel spectral radius is 0.9991612 estimated iterations to convergence 273 setup time was (sec) 1.690000 now iterating at: 03:20:33 rms-change max change #iterations 9.528935 307.9043 at 10iterations 5.399584 148.3579 at 20iterations 3.045547 76.19565 at 30iterations 1.711500 39.03688 at 40iterations 0.9597614 24.93553 at 50iterations 0.5362279 12.04420 at 60iterations 0.2994324 5.976986 at 70iterations 0.1666098 3.698129 at 80iterations 9.2771761E-02 1.899170 at 90iterations 5.1623635E-02 1.097466 at 100iterations 2.8663028E-02 0.5701122 at 110iterations 1.5956715E-02 0.3708172 at 120iterations 8.8594323E-03 0.1804829 at 130iterations 4.9224384E-03 0.1144863 at 140iterations 2.7494458E-03 5.7670593E-02 at 150iterations 1.5298187E-03 2.8716564E-02 at 160iterations 8.5934973E-04 1.6222954E-02 at 170iterations 4.8521350E-04 9.3885660E-03 at 180iterations finished qdiffx linear iterations at : 03:20:44 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 4.8521350E-04 9.3885660E-03 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 03:20:45 12.946u 0.205s 0:13.65 96.2% 0+0k 0+0io 0pf+0w