Tue Oct 11 06:49:41 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 06:49:41 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4070 !!! WARNING: GLM 87 has a net charge of -0.0940 !!! WARNING: SEP 189 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5035218 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): -8.484000 62.21800 ymin,ymax (A): 49.10600 109.4450 zmin,zma (A): 65.22300 112.9220 x,y,z range (A): 70.70200 60.33900 47.69901 scale (grids/A): 0.5035218 object centre (A): 26.86700 79.27550 89.07250 number of atom coordinates read : 4070 total number of charged atoms : 3918 net assigned charge : -2.568986 assigned positive charge : 614.2220 centred at (gu) : 89.37682 87.93832 89.41806 assigned negative charge : -616.7937 centred at (gu) : 89.50359 87.92575 89.49506 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6555 nv = 96 ne = 84 npr = 80745 no. pairs analyzed = 80745 no. exposed pairs = 5202 no. arc points = 36799 no. surface atoms = 1746 nbur = 2324 mkacc time = 0.2300000 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 = 1.708000 m= 242 mr = 3254 m= 0 mr = 6 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 3537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3509 ## 540 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 8767 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1374879E-10 -1.3295505E-10 midg,1,midg; midg,igrid,midg -8.4391390E-11 -4.6136137E-12 1,midg,midg; igrid,midg,midg 2.0900770E-10 -2.0232414E-10 gauss-seidel spectral radius is 0.9797894 estimated iterations to convergence 58 setup time was (sec) 0.7500000 now iterating at: 06:49:42 rms-change max change #iterations 5.7415262E-02 9.283796 at 10iterations 3.2963927E-03 0.6359406 at 20iterations 2.9819761E-04 4.2343140E-02 at 30iterations 5.3046275E-05 6.5097809E-03 at 40iterations 1.1301691E-05 1.3484955E-03 at 50iterations finished qdiffx linear iterations at : 06:49:45 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 1.1301691E-05 1.3484955E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 06:49:47 4.222u 0.255s 0:05.96 75.0% 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 06:49:47 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4070 !!! WARNING: GLM 87 has a net charge of -0.0940 !!! WARNING: SEP 189 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.510565 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): -8.484000 62.21800 ymin,ymax (A): 49.10600 109.4450 zmin,zma (A): 65.22300 112.9220 x,y,z range (A): 70.70200 60.33900 47.69901 scale (grids/A): 1.510565 object centre (A): 26.86700 79.27550 89.07250 number of atom coordinates read : 4070 total number of charged atoms : 3918 net assigned charge : -2.568986 assigned positive charge : 614.2220 centred at (gu) : 88.12915 83.81340 88.25311 assigned negative charge : -616.7937 centred at (gu) : 88.51036 83.77682 88.48478 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 74816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36799 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 20440 mr = 49939 m= 1551 mr = 13218 m= 26 mr = 557 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 343 time to turn everything in is 0.6700000 number of dielectric boundary points 33119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 496 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 29343 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) : 0.5035218 object centre at (A) : 26.86700 79.27550 89.07250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6159760E-03 -2.6142029E-03 midg,1,midg; midg,igrid,midg -7.6505258E-03 -4.1510509E-03 1,midg,midg; igrid,midg,midg 4.3815218E-02 9.1875521E-03 gauss-seidel spectral radius is 0.9979774 estimated iterations to convergence 177 setup time was (sec) 0.9700000 now iterating at: 06:49:48 rms-change max change #iterations 3.376468 159.8266 at 10iterations 1.341258 55.37761 at 20iterations 0.5330407 18.34079 at 30iterations 0.2122132 8.025640 at 40iterations 8.4563389E-02 3.071475 at 50iterations 3.3759404E-02 1.231969 at 60iterations 1.3395506E-02 0.4750133 at 70iterations 5.3517055E-03 0.2250519 at 80iterations 2.1416941E-03 8.2733154E-02 at 90iterations 8.6042512E-04 2.8778076E-02 at 100iterations 3.4720395E-04 1.3114691E-02 at 110iterations 1.4271372E-04 4.8294067E-03 at 120iterations finished qdiffx linear iterations at : 06:49:57 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 1.4271372E-04 4.8294067E-03 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 06:49:58 9.361u 0.288s 0:10.46 92.1% 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 06:49:58 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4070 !!! WARNING: GLM 87 has a net charge of -0.0940 !!! WARNING: SEP 189 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.265848 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): -8.484000 62.21800 ymin,ymax (A): 49.10600 109.4450 zmin,zma (A): 65.22300 112.9220 x,y,z range (A): 70.70200 60.33900 47.69901 scale (grids/A): 2.265848 object centre (A): 26.86700 79.27550 89.07250 number of atom coordinates read : 4070 total number of charged atoms : 3918 net assigned charge : -2.568986 assigned positive charge : 614.2220 centred at (gu) : 87.19347 80.71983 87.37933 assigned negative charge : -616.7937 centred at (gu) : 87.76540 80.66520 87.72709 start vw surface at 0.2000000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 174628 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36799 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 74811 mr = 123055 m= 17322 mr = 57544 m= 1984 mr = 12174 m= 60 mr = 1121 m= 0 mr = 12 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 1153 time to turn everything in is 1.610000 number of dielectric boundary points 74899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 31243 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) : 1.510565 object centre at (A) : 26.86700 79.27550 89.07250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4419119E-02 -5.3589642E-02 midg,1,midg; midg,igrid,midg -0.1066120 -5.4644097E-02 1,midg,midg; igrid,midg,midg 0.9656326 0.2140175 gauss-seidel spectral radius is 0.9991017 estimated iterations to convergence 264 setup time was (sec) 1.940000 now iterating at: 06:50:00 rms-change max change #iterations 9.254208 318.5836 at 10iterations 5.211661 157.8661 at 20iterations 2.911202 93.52188 at 30iterations 1.617305 43.45625 at 40iterations 0.8931600 25.67438 at 50iterations 0.4915298 14.76654 at 60iterations 0.2699805 6.665301 at 70iterations 0.1482421 3.809129 at 80iterations 8.1074797E-02 1.962466 at 90iterations 4.4316180E-02 0.9988661 at 100iterations 2.4180500E-02 0.6152973 at 110iterations 1.3178619E-02 0.3143630 at 120iterations 7.1861083E-03 0.1660004 at 130iterations 3.9123078E-03 9.7483397E-02 at 140iterations 2.1315988E-03 4.1233301E-02 at 150iterations 1.1595738E-03 2.6666641E-02 at 160iterations 6.3050754E-04 1.4563560E-02 at 170iterations 3.4326976E-04 7.3208809E-03 at 180iterations finished qdiffx linear iterations at : 06:50:14 total time elapsed so far: 15.45000 # loops : 180 mean,max change (kT/e) : 3.4326976E-04 7.3208809E-03 energy calculations done at 15.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.63000 DelPhi exited at 06:50:14 15.633u 0.289s 0:16.47 96.5% 0+0k 0+0io 0pf+0w