Mon Oct 10 00:40:58 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 00:40:58 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2156 !!! WARNING: HIT 115 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6944038 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): -9.444000 40.42800 ymin,ymax (A): -54.37400 -11.23500 zmin,zma (A): -28.29200 22.97500 x,y,z range (A): 49.87200 43.13900 51.26700 scale (grids/A): 0.6944038 object centre (A): 15.49200 -32.80450 -2.658500 number of atom coordinates read : 2156 total number of charged atoms : 2014 net assigned charge : 3.014005 assigned positive charge : 323.5207 centred at (gu) : 89.90208 89.66259 88.63264 assigned negative charge : -320.5069 centred at (gu) : 89.95593 89.67199 88.53829 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7377 nv = 96 ne = 84 npr = 42210 no. pairs analyzed = 42210 no. exposed pairs = 2964 no. arc points = 20613 no. surface atoms = 995 nbur = 1161 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 490 mr = 3964 m= 2 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1785 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2679094E-08 4.1473132E-08 midg,1,midg; midg,igrid,midg 2.4151065E-08 1.4578876E-08 1,midg,midg; igrid,midg,midg 4.0038184E-08 -1.2807914E-09 gauss-seidel spectral radius is 0.9892160 estimated iterations to convergence 78 setup time was (sec) 0.5300000 now iterating at: 00:40:59 rms-change max change #iterations 0.1933697 30.05784 at 10iterations 2.2754190E-02 3.550314 at 20iterations 2.6737868E-03 0.3344760 at 30iterations 3.2040678E-04 4.6421051E-02 at 40iterations 3.9919589E-05 5.1574707E-03 at 50iterations finished qdiffx linear iterations at : 00:41:02 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 3.9919589E-05 5.1574707E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 00:41:02 3.296u 0.143s 0:03.72 92.2% 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 00:41:02 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2156 !!! WARNING: HIT 115 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.083211 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): -9.444000 40.42800 ymin,ymax (A): -54.37400 -11.23500 zmin,zma (A): -28.29200 22.97500 x,y,z range (A): 49.87200 43.13900 51.26700 scale (grids/A): 2.083211 object centre (A): 15.49200 -32.80450 -2.658500 number of atom coordinates read : 2156 total number of charged atoms : 2014 net assigned charge : 3.014005 assigned positive charge : 323.5207 centred at (gu) : 89.70638 88.98766 85.89750 assigned negative charge : -320.5069 centred at (gu) : 89.86790 89.01595 85.61474 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20613 grid for indexing accessible points = 1.400000 m= 29974 mr = 52764 m= 6469 mr = 22190 m= 644 mr = 4600 m= 12 mr = 348 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 34940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 15970 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) : 0.6944038 object centre at (A) : 15.49200 -32.80450 -2.658500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5900716E-02 6.5719739E-02 midg,1,midg; midg,igrid,midg 1.0427064E-02 8.8552460E-03 1,midg,midg; igrid,midg,midg 2.2066748E-02 -1.5738234E-02 gauss-seidel spectral radius is 0.9988223 estimated iterations to convergence 231 setup time was (sec) 0.8700000 now iterating at: 00:41:03 rms-change max change #iterations 4.664208 187.1375 at 10iterations 2.302938 76.27721 at 20iterations 1.146530 37.31398 at 30iterations 0.5709820 18.36981 at 40iterations 0.2834172 8.757813 at 50iterations 0.1407467 4.652826 at 60iterations 6.9354750E-02 2.027508 at 70iterations 3.4492154E-02 1.072535 at 80iterations 1.7163157E-02 0.5606018 at 90iterations 8.4725060E-03 0.2881203 at 100iterations 4.2213858E-03 0.1220322 at 110iterations 2.0861726E-03 6.2547684E-02 at 120iterations finished qdiffx linear iterations at : 00:41:10 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 2.0861726E-03 6.2547684E-02 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 00:41:10 7.489u 0.160s 0:07.98 95.7% 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 00:41:10 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2156 !!! WARNING: HIT 115 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.124817 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): -9.444000 40.42800 ymin,ymax (A): -54.37400 -11.23500 zmin,zma (A): -28.29200 22.97500 x,y,z range (A): 49.87200 43.13900 51.26700 scale (grids/A): 3.124817 object centre (A): 15.49200 -32.80450 -2.658500 number of atom coordinates read : 2156 total number of charged atoms : 2014 net assigned charge : 3.014005 assigned positive charge : 323.5207 centred at (gu) : 89.55949 88.48141 83.84617 assigned negative charge : -320.5069 centred at (gu) : 89.80183 88.52404 83.42199 start vw surface at 0.1400000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 179234 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20613 grid for indexing accessible points = 1.400000 m= 92383 mr = 127657 m= 38562 mr = 75056 m= 12700 mr = 31741 m= 2845 mr = 10286 m= 327 mr = 2213 m= 16 mr = 226 m= 0 mr = 6 time to grow re-entrant surface = 0.9200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 78882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 16112 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) : 2.083211 object centre at (A) : 15.49200 -32.80450 -2.658500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6437757 0.9695347 midg,1,midg; midg,igrid,midg 4.4133101E-02 6.5408610E-02 1,midg,midg; igrid,midg,midg 0.3961470 -5.1881600E-02 gauss-seidel spectral radius is 0.9993149 estimated iterations to convergence 301 setup time was (sec) 2.160000 now iterating at: 00:41:12 rms-change max change #iterations 10.51651 397.1309 at 10iterations 6.272974 143.4504 at 20iterations 3.737104 77.95201 at 30iterations 2.223635 43.08897 at 40iterations 1.316226 25.01092 at 50iterations 0.7800667 13.86761 at 60iterations 0.4606443 7.731735 at 70iterations 0.2718283 5.149058 at 80iterations 0.1601316 3.345825 at 90iterations 9.4302610E-02 1.685946 at 100iterations 5.5446249E-02 1.001577 at 110iterations 3.2660786E-02 0.5716610 at 120iterations 1.9187232E-02 0.3199258 at 130iterations 1.1286595E-02 0.1814966 at 140iterations 6.6345842E-03 0.1100614 at 150iterations 3.8929977E-03 6.3560486E-02 at 160iterations 2.2902437E-03 4.1839600E-02 at 170iterations 1.3458329E-03 2.2445679E-02 at 180iterations finished qdiffx linear iterations at : 00:41:23 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 1.3458329E-03 2.2445679E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 00:41:23 12.681u 0.174s 0:13.14 97.7% 0+0k 0+0io 0pf+0w