Sun Oct 9 11:51:17 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 Sun Oct 9 2011 at 11:51:17 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 !!! WARNING: HIR 203 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6706352 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): -4.628000 47.87900 ymin,ymax (A): 9.092000 60.33200 zmin,zma (A): 4.487000 57.57100 x,y,z range (A): 52.50700 51.24000 53.08400 scale (grids/A): 0.6706352 object centre (A): 21.62550 34.71200 31.02900 number of atom coordinates read : 2747 total number of charged atoms : 2675 net assigned charge : 2.514010 assigned positive charge : 412.6390 centred at (gu) : 90.75077 89.98355 91.64216 assigned negative charge : -410.1266 centred at (gu) : 90.81169 89.94468 91.58163 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8870 nv = 96 ne = 84 npr = 52296 no. pairs analyzed = 52296 no. exposed pairs = 3841 no. arc points = 27531 no. surface atoms = 1277 nbur = 1470 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 575 mr = 4579 m= 6 mr = 105 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 0.2900000 number of dielectric boundary points 4767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2493 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10121 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7883360E-09 3.4721413E-08 midg,1,midg; midg,igrid,midg -2.3455737E-09 1.8791615E-08 1,midg,midg; igrid,midg,midg 2.1274296E-08 -9.9373487E-09 gauss-seidel spectral radius is 0.9885093 estimated iterations to convergence 76 setup time was (sec) 0.4900000 now iterating at: 11:51:18 rms-change max change #iterations 0.1832015 23.78034 at 10iterations 2.0133603E-02 3.055675 at 20iterations 2.2067856E-03 0.2799883 at 30iterations 2.4497215E-04 3.5850525E-02 at 40iterations 3.3070948E-05 4.7874451E-03 at 50iterations finished qdiffx linear iterations at : 11:51:21 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.3070948E-05 4.7874451E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 11:51:21 3.387u 0.146s 0:03.85 91.4% 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 Sun Oct 9 2011 at 11:51:21 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 = 2747 !!! WARNING: HIR 203 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: 2.011906 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): -4.628000 47.87900 ymin,ymax (A): 9.092000 60.33200 zmin,zma (A): 4.487000 57.57100 x,y,z range (A): 52.50700 51.24000 53.08400 scale (grids/A): 2.011906 object centre (A): 21.62550 34.71200 31.02900 number of atom coordinates read : 2747 total number of charged atoms : 2675 net assigned charge : 2.514010 assigned positive charge : 412.6390 centred at (gu) : 92.25132 89.94984 94.92580 assigned negative charge : -410.1266 centred at (gu) : 92.43517 89.83393 94.74505 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 93553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27531 grid for indexing accessible points = 1.400000 m= 35907 mr = 62660 m= 7578 mr = 25824 m= 741 mr = 4952 m= 18 mr = 352 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 44009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 21211 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) : 0.6706352 object centre at (A) : 21.62550 34.71200 31.02900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5709692E-03 4.9030505E-02 midg,1,midg; midg,igrid,midg -1.4232331E-02 3.1699713E-02 1,midg,midg; igrid,midg,midg 3.3870828E-04 1.5900927E-04 gauss-seidel spectral radius is 0.9988156 estimated iterations to convergence 230 setup time was (sec) 0.9200000 now iterating at: 11:51:22 rms-change max change #iterations 4.899505 220.7636 at 10iterations 2.405459 82.31629 at 20iterations 1.180626 35.01239 at 30iterations 0.5830771 16.46677 at 40iterations 0.2870871 7.822936 at 50iterations 0.1414357 4.160067 at 60iterations 6.9534324E-02 2.107383 at 70iterations 3.4364775E-02 0.9865036 at 80iterations 1.6910970E-02 0.4849930 at 90iterations 8.3570108E-03 0.2540364 at 100iterations 4.1103801E-03 0.1268232 at 110iterations 2.0312080E-03 5.5334091E-02 at 120iterations finished qdiffx linear iterations at : 11:51:29 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 2.0312080E-03 5.5334091E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 11:51:30 8.027u 0.177s 0:08.52 96.1% 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 Sun Oct 9 2011 at 11:51:30 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 = 2747 !!! WARNING: HIR 203 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.017859 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): -4.628000 47.87900 ymin,ymax (A): 9.092000 60.33200 zmin,zma (A): 4.487000 57.57100 x,y,z range (A): 52.50700 51.24000 53.08400 scale (grids/A): 3.017859 object centre (A): 21.62550 34.71200 31.02900 number of atom coordinates read : 2747 total number of charged atoms : 2675 net assigned charge : 2.514010 assigned positive charge : 412.6390 centred at (gu) : 93.37679 89.92450 97.38857 assigned negative charge : -410.1266 centred at (gu) : 93.65271 89.75074 97.11745 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 215699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27531 grid for indexing accessible points = 1.400000 m= 110282 mr = 151985 m= 46149 mr = 88305 m= 14387 mr = 36856 m= 3058 mr = 11049 m= 343 mr = 2259 m= 12 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.720000 number of dielectric boundary points 99282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 21400 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) : 2.011906 object centre at (A) : 21.62550 34.71200 31.02900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7815631E-02 0.5569811 midg,1,midg; midg,igrid,midg -9.6350797E-02 0.3877232 1,midg,midg; igrid,midg,midg -5.2194905E-02 0.3043438 gauss-seidel spectral radius is 0.9993331 estimated iterations to convergence 305 setup time was (sec) 2.060000 now iterating at: 11:51:32 rms-change max change #iterations 11.41322 428.2406 at 10iterations 6.957133 139.7301 at 20iterations 4.217250 90.03381 at 30iterations 2.542719 57.42198 at 40iterations 1.526938 27.80006 at 50iterations 0.9142153 15.75343 at 60iterations 0.5464169 9.848446 at 70iterations 0.3247007 5.985203 at 80iterations 0.1934373 3.256197 at 90iterations 0.1149917 1.972042 at 100iterations 6.8414807E-02 1.102264 at 110iterations 4.0458359E-02 0.6616755 at 120iterations 2.4042832E-02 0.3927965 at 130iterations 1.4240704E-02 0.2355421 at 140iterations 8.4369080E-03 0.1479034 at 150iterations 5.0005661E-03 8.3232880E-02 at 160iterations 2.9676754E-03 4.9163818E-02 at 170iterations 1.7518487E-03 2.8951645E-02 at 180iterations finished qdiffx linear iterations at : 11:51:44 total time elapsed so far: 14.07000 # loops : 180 mean,max change (kT/e) : 1.7518487E-03 2.8951645E-02 energy calculations done at 14.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.28000 DelPhi exited at 11:51:45 14.279u 0.283s 0:14.90 97.6% 0+0k 0+0io 0pf+0w