Sat Oct 8 11:34:23 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 11:34:23 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2312 !!! WARNING: ASL 83 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6600904 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): -60.45900 -10.71600 ymin,ymax (A): 53.97600 102.4800 zmin,zma (A): 39.07800 93.01000 x,y,z range (A): 49.74300 48.50399 53.93200 scale (grids/A): 0.6600904 object centre (A): -35.58750 78.22800 66.04400 number of atom coordinates read : 2312 total number of charged atoms : 2155 net assigned charge : -1.099996 assigned positive charge : 333.0084 centred at (gu) : 91.76711 90.47894 91.62200 assigned negative charge : -334.1086 centred at (gu) : 91.68069 90.45961 91.62893 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7049 nv = 96 ne = 84 npr = 47128 no. pairs analyzed = 47128 no. exposed pairs = 3076 no. arc points = 21499 no. surface atoms = 1038 nbur = 1274 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 408 mr = 3775 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1995 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7984 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3832074E-09 -5.9315237E-09 midg,1,midg; midg,igrid,midg -5.7551657E-09 2.4784730E-10 1,midg,midg; igrid,midg,midg -1.2364836E-08 1.6839129E-08 gauss-seidel spectral radius is 0.9880878 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 11:34:24 rms-change max change #iterations 0.1533822 20.84989 at 10iterations 1.6602462E-02 2.655762 at 20iterations 1.7480326E-03 0.2468758 at 30iterations 1.8325060E-04 2.7168274E-02 at 40iterations 1.9825098E-05 2.9487610E-03 at 50iterations finished qdiffx linear iterations at : 11:34:27 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 1.9825098E-05 2.9487610E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 11:34:27 3.620u 0.203s 0:04.09 93.3% 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 11:34:27 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2312 !!! WARNING: ASL 83 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.980271 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): -60.45900 -10.71600 ymin,ymax (A): 53.97600 102.4800 zmin,zma (A): 39.07800 93.01000 x,y,z range (A): 49.74300 48.50399 53.93200 scale (grids/A): 1.980271 object centre (A): -35.58750 78.22800 66.04400 number of atom coordinates read : 2312 total number of charged atoms : 2155 net assigned charge : -1.099996 assigned positive charge : 333.0084 centred at (gu) : 95.30105 91.43674 94.86575 assigned negative charge : -334.1086 centred at (gu) : 95.04187 91.37862 94.88657 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21499 grid for indexing accessible points = 1.400000 m= 26753 mr = 50892 m= 4288 mr = 19354 m= 259 mr = 2601 m= 8 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 33499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17032 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) : 0.6600904 object centre at (A) : -35.58750 78.22800 66.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4012720E-02 3.6436170E-03 midg,1,midg; midg,igrid,midg -1.5327631E-02 -1.5292014E-02 1,midg,midg; igrid,midg,midg -1.0197220E-02 2.6282964E-02 gauss-seidel spectral radius is 0.9987088 estimated iterations to convergence 220 setup time was (sec) 0.6200000 now iterating at: 11:34:28 rms-change max change #iterations 4.173444 175.6126 at 10iterations 1.986086 75.87778 at 20iterations 0.9499685 30.21227 at 30iterations 0.4513147 14.69468 at 40iterations 0.2165820 8.139383 at 50iterations 0.1033735 3.131088 at 60iterations 4.9207259E-02 1.491816 at 70iterations 2.3434194E-02 0.7520261 at 80iterations 1.1230796E-02 0.3512564 at 90iterations 5.3444440E-03 0.1654625 at 100iterations 2.5575901E-03 9.1513634E-02 at 110iterations 1.2234693E-03 4.2464256E-02 at 120iterations finished qdiffx linear iterations at : 11:34:42 total time elapsed so far: 9.910000 # loops : 120 mean,max change (kT/e) : 1.2234693E-03 4.2464256E-02 energy calculations done at 9.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.05000 DelPhi exited at 11:34:43 10.050u 0.312s 0:15.08 68.7% 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 Sat Oct 8 2011 at 11:34:43 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2312 !!! WARNING: ASL 83 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.970407 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): -60.45900 -10.71600 ymin,ymax (A): 53.97600 102.4800 zmin,zma (A): 39.07800 93.01000 x,y,z range (A): 49.74300 48.50399 53.93200 scale (grids/A): 2.970407 object centre (A): -35.58750 78.22800 66.04400 number of atom coordinates read : 2312 total number of charged atoms : 2155 net assigned charge : -1.099996 assigned positive charge : 333.0084 centred at (gu) : 97.95141 92.15503 97.29848 assigned negative charge : -334.1086 centred at (gu) : 97.56280 92.06787 97.32982 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 173785 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21499 grid for indexing accessible points = 1.400000 m= 86057 mr = 123853 m= 31234 mr = 69500 m= 7587 mr = 24605 m= 1134 mr = 5607 m= 69 mr = 708 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9700000 number of dielectric boundary points 75568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 17240 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) : 1.980271 object centre at (A) : -35.58750 78.22800 66.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3941907 -3.1153552E-02 midg,1,midg; midg,igrid,midg -0.1348307 -0.1676301 1,midg,midg; igrid,midg,midg -0.1344997 0.2741427 gauss-seidel spectral radius is 0.9992833 estimated iterations to convergence 295 setup time was (sec) 1.240000 now iterating at: 11:34:44 rms-change max change #iterations 9.831903 417.3358 at 10iterations 5.817726 137.6572 at 20iterations 3.428399 82.10746 at 30iterations 2.014037 44.83350 at 40iterations 1.175735 27.83500 at 50iterations 0.6884222 14.20488 at 60iterations 0.4017712 8.215858 at 70iterations 0.2343290 4.471931 at 80iterations 0.1361623 2.613795 at 90iterations 7.9099707E-02 1.584666 at 100iterations 4.5930266E-02 0.8790016 at 110iterations 2.6766654E-02 0.4954529 at 120iterations 1.5526090E-02 0.2942257 at 130iterations 9.0217339E-03 0.1774826 at 140iterations 5.2283397E-03 9.7808838E-02 at 150iterations 3.0392439E-03 6.0055494E-02 at 160iterations 1.7600695E-03 3.1307220E-02 at 170iterations 1.0208746E-03 1.9787788E-02 at 180iterations finished qdiffx linear iterations at : 11:34:57 total time elapsed so far: 13.94000 # loops : 180 mean,max change (kT/e) : 1.0208746E-03 1.9787788E-02 energy calculations done at 13.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.08000 DelPhi exited at 11:34:58 14.085u 0.276s 0:15.32 93.6% 0+0k 0+0io 0pf+0w