Sun Oct 9 20:06:23 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 Sun Oct 9 2011 at 20:06:23 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5118 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5465907 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): 3.355000 68.48600 ymin,ymax (A): -8.921000 53.69300 zmin,zma (A): -0.9150000 63.85900 x,y,z range (A): 65.13100 62.61400 64.77400 scale (grids/A): 0.5465907 object centre (A): 35.92050 22.38600 31.47200 number of atom coordinates read : 5118 total number of charged atoms : 4964 net assigned charge : 0.5440479 assigned positive charge : 783.7523 centred at (gu) : 87.88453 89.24805 89.07877 assigned negative charge : -783.2137 centred at (gu) : 87.77235 89.27965 89.05885 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 10189 nv = 96 ne = 84 npr = 102218 no. pairs analyzed = 102218 no. exposed pairs = 6039 no. arc points = 41536 no. surface atoms = 2052 nbur = 3066 mkacc time = 0.1900000 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 = 1.568000 m= 437 mr = 5847 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4227 ## 500 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 13331 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1674390E-10 2.4026015E-10 midg,1,midg; midg,igrid,midg 5.3164784E-10 -2.5729413E-10 1,midg,midg; igrid,midg,midg -2.2073476E-09 8.1706397E-10 gauss-seidel spectral radius is 0.9829028 estimated iterations to convergence 63 setup time was (sec) 0.5600000 now iterating at: 20:06:23 rms-change max change #iterations 0.1061035 14.48912 at 10iterations 1.2184836E-02 1.504562 at 20iterations 4.8323371E-03 0.7048874 at 30iterations 2.3476298E-03 0.3515511 at 40iterations 1.1510242E-03 0.1730194 at 50iterations finished qdiffx linear iterations at : 20:06:26 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 1.1510242E-03 0.1730194 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 20:06:27 3.636u 0.226s 0:04.32 89.1% 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 20:06:27 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5118 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.639772 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): 3.355000 68.48600 ymin,ymax (A): -8.921000 53.69300 zmin,zma (A): -0.9150000 63.85900 x,y,z range (A): 65.13100 62.61400 64.77400 scale (grids/A): 1.639772 object centre (A): 35.92050 22.38600 31.47200 number of atom coordinates read : 5118 total number of charged atoms : 4964 net assigned charge : 0.5440479 assigned positive charge : 783.7523 centred at (gu) : 83.65232 87.74262 87.23503 assigned negative charge : -783.2137 centred at (gu) : 83.31701 87.83863 87.17655 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 114353 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 39579 mr = 82994 m= 4656 mr = 28786 m= 142 mr = 2488 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.5600000 number of dielectric boundary points 44438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 416 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 38064 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) : 0.5465907 object centre at (A) : 35.92050 22.38600 31.47200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3367828E-02 -1.2728072E-02 midg,1,midg; midg,igrid,midg 2.0312520E-02 9.8067997E-03 1,midg,midg; igrid,midg,midg -2.0511616E-02 1.8496703E-02 gauss-seidel spectral radius is 0.9984021 estimated iterations to convergence 199 setup time was (sec) 0.7900000 now iterating at: 20:06:28 rms-change max change #iterations 4.731390 179.6796 at 10iterations 2.080082 60.95792 at 20iterations 0.9200242 26.60668 at 30iterations 0.4057842 10.44946 at 40iterations 0.1798959 4.958843 at 50iterations 8.0358677E-02 2.602509 at 60iterations 3.7079602E-02 1.090973 at 70iterations 1.8159395E-02 0.5480537 at 80iterations 1.0186764E-02 0.3277206 at 90iterations 6.5492271E-03 0.2060089 at 100iterations 4.6701324E-03 0.1411133 at 110iterations 3.5121050E-03 0.1034775 at 120iterations finished qdiffx linear iterations at : 20:06:36 total time elapsed so far: 8.280000 # loops : 120 mean,max change (kT/e) : 3.5121050E-03 0.1034775 energy calculations done at 8.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.410000 DelPhi exited at 20:06:37 8.415u 0.937s 0:09.77 95.5% 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 20:06:37 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5118 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.459658 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): 3.355000 68.48600 ymin,ymax (A): -8.921000 53.69300 zmin,zma (A): -0.9150000 63.85900 x,y,z range (A): 65.13100 62.61400 64.77400 scale (grids/A): 2.459658 object centre (A): 35.92050 22.38600 31.47200 number of atom coordinates read : 5118 total number of charged atoms : 4964 net assigned charge : 0.5440479 assigned positive charge : 783.7523 centred at (gu) : 80.47820 86.61370 85.85219 assigned negative charge : -783.2137 centred at (gu) : 79.97540 86.75812 85.76492 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 265874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 134658 mr = 201968 m= 41489 mr = 110136 m= 7511 mr = 32279 m= 597 mr = 5192 m= 12 mr = 337 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 337 time to turn everything in is 1.410000 number of dielectric boundary points 100229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 39667 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) : 1.639772 object centre at (A) : 35.92050 22.38600 31.47200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5120692 -0.2664677 midg,1,midg; midg,igrid,midg 0.1937999 3.5082866E-02 1,midg,midg; igrid,midg,midg -0.4946074 0.2682411 gauss-seidel spectral radius is 0.9992480 estimated iterations to convergence 288 setup time was (sec) 1.680000 now iterating at: 20:06:39 rms-change max change #iterations 12.03333 318.1941 at 10iterations 7.080046 137.9096 at 20iterations 4.129633 81.59094 at 30iterations 2.402336 53.56190 at 40iterations 1.393143 27.97263 at 50iterations 0.8054635 15.35183 at 60iterations 0.4657144 8.132673 at 70iterations 0.2687125 4.344899 at 80iterations 0.1548641 2.532459 at 90iterations 8.9457273E-02 1.720103 at 100iterations 5.1850911E-02 0.8012390 at 110iterations 3.0475661E-02 0.5103989 at 120iterations 1.8279765E-02 0.3669415 at 130iterations 1.1412160E-02 0.1973915 at 140iterations 7.5683463E-03 0.1318436 at 150iterations 5.4201242E-03 0.1120148 at 160iterations 4.1529527E-03 7.7941895E-02 at 170iterations 3.3332629E-03 6.1189651E-02 at 180iterations finished qdiffx linear iterations at : 20:06:52 total time elapsed so far: 13.71000 # loops : 180 mean,max change (kT/e) : 3.3332629E-03 6.1189651E-02 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.86000 DelPhi exited at 20:06:52 13.857u 1.121s 0:15.25 98.1% 0+0k 0+0io 0pf+0w