Sat Oct 8 12:15:20 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 12:15:20 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 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: 0.5083172 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): -60.18700 9.848000 ymin,ymax (A): -37.65800 17.91700 zmin,zma (A): -4.185000 54.49700 x,y,z range (A): 70.03500 55.57500 58.68200 scale (grids/A): 0.5083172 object centre (A): -25.16950 -9.870501 25.15600 number of atom coordinates read : 2993 total number of charged atoms : 2854 net assigned charge : 1.000018 assigned positive charge : 414.2553 centred at (gu) : 93.38161 89.69901 89.58112 assigned negative charge : -413.2564 centred at (gu) : 93.20365 89.58549 89.54225 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5178 nv = 96 ne = 84 npr = 60248 no. pairs analyzed = 60248 no. exposed pairs = 4443 no. arc points = 31400 no. surface atoms = 1482 nbur = 1511 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 = 1.680000 m= 155 mr = 2091 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3037 ## 373 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 6726 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3520660E-11 5.0554182E-11 midg,1,midg; midg,igrid,midg -1.6261302E-10 1.4261929E-10 1,midg,midg; igrid,midg,midg -9.8130032E-11 5.9914163E-10 gauss-seidel spectral radius is 0.9801039 estimated iterations to convergence 59 setup time was (sec) 0.6500000 now iterating at: 12:15:21 rms-change max change #iterations 4.6920329E-02 8.524845 at 10iterations 4.2812265E-03 0.9128380 at 20iterations 1.2879085E-03 0.3172874 at 30iterations 4.6786721E-04 0.1152115 at 40iterations 1.7062246E-04 4.2030334E-02 at 50iterations finished qdiffx linear iterations at : 12:15:25 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 1.7062246E-04 4.2030334E-02 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 12:15:25 4.202u 0.271s 0:04.74 94.3% 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 12:15:25 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 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: 1.524952 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): -60.18700 9.848000 ymin,ymax (A): -37.65800 17.91700 zmin,zma (A): -4.185000 54.49700 x,y,z range (A): 70.03500 55.57500 58.68200 scale (grids/A): 1.524952 object centre (A): -25.16950 -9.870501 25.15600 number of atom coordinates read : 2993 total number of charged atoms : 2854 net assigned charge : 1.000018 assigned positive charge : 414.2553 centred at (gu) : 100.1440 89.09637 88.74259 assigned negative charge : -413.2564 centred at (gu) : 99.61058 88.75626 88.62651 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 57271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31400 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 14747 mr = 34511 m= 1269 mr = 8299 m= 16 mr = 420 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 30073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 275 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 21492 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) : 0.5083172 object centre at (A) : -25.16950 -9.870501 25.15600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9700036E-03 6.8976367E-03 midg,1,midg; midg,igrid,midg -3.9221132E-03 5.7524131E-03 1,midg,midg; igrid,midg,midg -2.4907966E-03 5.6102723E-03 gauss-seidel spectral radius is 0.9979287 estimated iterations to convergence 175 setup time was (sec) 0.8600000 now iterating at: 12:15:26 rms-change max change #iterations 2.709761 184.4031 at 10iterations 1.053278 45.80425 at 20iterations 0.4119220 18.29045 at 30iterations 0.1610165 6.576168 at 40iterations 6.3293561E-02 2.604513 at 50iterations 2.5340745E-02 1.045969 at 60iterations 1.0526881E-02 0.4639473 at 70iterations 4.8549185E-03 0.2265549 at 80iterations 2.6202931E-03 0.1345520 at 90iterations 1.6538410E-03 8.3152771E-02 at 100iterations 1.1303885E-03 5.5629730E-02 at 110iterations 7.9305680E-04 3.9424896E-02 at 120iterations finished qdiffx linear iterations at : 12:15:35 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 7.9305680E-04 3.9424896E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 12:15:35 9.372u 0.295s 0:09.96 96.9% 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 12:15:35 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 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: 2.287428 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): -60.18700 9.848000 ymin,ymax (A): -37.65800 17.91700 zmin,zma (A): -4.185000 54.49700 x,y,z range (A): 70.03500 55.57500 58.68200 scale (grids/A): 2.287428 object centre (A): -25.16950 -9.870501 25.15600 number of atom coordinates read : 2993 total number of charged atoms : 2854 net assigned charge : 1.000018 assigned positive charge : 414.2553 centred at (gu) : 105.2158 88.64447 88.11365 assigned negative charge : -413.2564 centred at (gu) : 104.4158 88.13435 87.93961 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 133328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31400 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 52599 mr = 86696 m= 12719 mr = 36802 m= 1678 mr = 8125 m= 47 mr = 855 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 67891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 22770 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) : 1.524952 object centre at (A) : -25.16950 -9.870501 25.15600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2171433E-03 0.1131080 midg,1,midg; midg,igrid,midg -7.1841240E-02 9.2697769E-02 1,midg,midg; igrid,midg,midg -3.0094687E-02 0.1400071 gauss-seidel spectral radius is 0.9990599 estimated iterations to convergence 258 setup time was (sec) 1.600000 now iterating at: 12:15:37 rms-change max change #iterations 7.491607 249.2681 at 10iterations 4.170910 130.4615 at 20iterations 2.310343 67.39168 at 30iterations 1.266756 32.70230 at 40iterations 0.6915762 18.93660 at 50iterations 0.3750433 9.192560 at 60iterations 0.2042930 5.472364 at 70iterations 0.1103773 2.737456 at 80iterations 5.9595205E-02 1.467086 at 90iterations 3.2179736E-02 0.8791776 at 100iterations 1.7409487E-02 0.3971043 at 110iterations 9.4575062E-03 0.2173328 at 120iterations 5.1901415E-03 0.1320801 at 130iterations 2.9131728E-03 7.1609497E-02 at 140iterations 1.7121832E-03 4.4879913E-02 at 150iterations 1.0804872E-03 3.0410767E-02 at 160iterations 7.3725492E-04 2.2556305E-02 at 170iterations 5.3803722E-04 1.5716553E-02 at 180iterations finished qdiffx linear iterations at : 12:15:51 total time elapsed so far: 15.26000 # loops : 180 mean,max change (kT/e) : 5.3803722E-04 1.5716553E-02 energy calculations done at 15.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.43000 DelPhi exited at 12:15:51 15.435u 0.332s 0:16.03 98.3% 0+0k 0+0io 0pf+0w