Tue Oct 11 06:13:08 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+sph.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 = amb.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 06:13:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2027 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7480248 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): -17.97200 28.39700 ymin,ymax (A): -11.77700 31.09100 zmin,zma (A): -8.937000 38.65500 x,y,z range (A): 46.36900 42.86800 47.59200 scale (grids/A): 0.7480248 object centre (A): 5.212500 9.657000 14.85900 number of atom coordinates read : 2027 total number of charged atoms : 1914 net assigned charge : 7.500009 assigned positive charge : 309.6501 centred at (gu) : 90.51298 89.98172 90.78523 assigned negative charge : -302.1502 centred at (gu) : 90.37839 89.91602 90.65817 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7937 nv = 96 ne = 84 npr = 40053 no. pairs analyzed = 40053 no. exposed pairs = 2539 no. arc points = 17401 no. surface atoms = 856 nbur = 1171 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 637 mr = 4655 m= 4 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2400000 number of dielectric boundary points 3780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1505 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 8238 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9239958E-09 3.4291457E-07 midg,1,midg; midg,igrid,midg 8.0752081E-08 2.2791032E-07 1,midg,midg; igrid,midg,midg 2.0855146E-09 3.3517344E-07 gauss-seidel spectral radius is 0.9906724 estimated iterations to convergence 84 setup time was (sec) 0.4500000 now iterating at: 06:13:09 rms-change max change #iterations 0.2511777 28.57171 at 10iterations 3.4897130E-02 4.231513 at 20iterations 4.9646390E-03 0.6346312 at 30iterations 7.6296611E-04 8.8045120E-02 at 40iterations 1.6538870E-04 2.0540237E-02 at 50iterations finished qdiffx linear iterations at : 06:13:11 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 1.6538870E-04 2.0540237E-02 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.010000 DelPhi exited at 06:13:12 3.016u 0.147s 0:03.65 86.3% 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 Tue Oct 11 2011 at 06:13:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2027 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: 2.244075 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): -17.97200 28.39700 ymin,ymax (A): -11.77700 31.09100 zmin,zma (A): -8.937000 38.65500 x,y,z range (A): 46.36900 42.86800 47.59200 scale (grids/A): 2.244075 object centre (A): 5.212500 9.657000 14.85900 number of atom coordinates read : 2027 total number of charged atoms : 1914 net assigned charge : 7.500009 assigned positive charge : 309.6501 centred at (gu) : 91.53916 89.94543 92.35608 assigned negative charge : -302.1502 centred at (gu) : 91.13519 89.74828 91.97467 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82804 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17401 grid for indexing accessible points = 1.400000 m= 36337 mr = 59143 m= 8539 mr = 28113 m= 1074 mr = 6000 m= 55 mr = 601 m= 0 mr = 9 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 398 time to turn everything in is 0.6300000 number of dielectric boundary points 34943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 15256 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) : 0.7480248 object centre at (A) : 5.212500 9.657000 14.85900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8611738E-02 5.2480184E-02 midg,1,midg; midg,igrid,midg 3.4707148E-02 3.3811912E-02 1,midg,midg; igrid,midg,midg 4.2420201E-02 0.1127937 gauss-seidel spectral radius is 0.9989342 estimated iterations to convergence 242 setup time was (sec) 0.9100000 now iterating at: 06:13:13 rms-change max change #iterations 4.974143 191.7830 at 10iterations 2.557442 84.23753 at 20iterations 1.303948 39.07959 at 30iterations 0.6696385 18.19967 at 40iterations 0.3417512 9.231298 at 50iterations 0.1755733 4.766921 at 60iterations 8.9715466E-02 2.835555 at 70iterations 4.6184506E-02 1.289502 at 80iterations 2.3747375E-02 0.7271237 at 90iterations 1.2212958E-02 0.3582077 at 100iterations 6.3110543E-03 0.1769428 at 110iterations 3.2975636E-03 8.9889526E-02 at 120iterations finished qdiffx linear iterations at : 06:13:19 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 3.2975636E-03 8.9889526E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.030000 DelPhi exited at 06:13:20 7.035u 0.181s 0:07.70 93.6% 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 06:13:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2027 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.366112 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): -17.97200 28.39700 ymin,ymax (A): -11.77700 31.09100 zmin,zma (A): -8.937000 38.65500 x,y,z range (A): 46.36900 42.86800 47.59200 scale (grids/A): 3.366112 object centre (A): 5.212500 9.657000 14.85900 number of atom coordinates read : 2027 total number of charged atoms : 1914 net assigned charge : 7.500009 assigned positive charge : 309.6501 centred at (gu) : 92.30876 89.91798 93.53408 assigned negative charge : -302.1502 centred at (gu) : 91.70286 89.62237 92.96205 start vw surface at 0.1500000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 190615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17401 grid for indexing accessible points = 1.400000 m= 108901 mr = 142110 m= 49955 mr = 91536 m= 16582 mr = 41743 m= 4128 mr = 13197 m= 633 mr = 3096 m= 72 mr = 407 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 1518 time to turn everything in is 1.980000 number of dielectric boundary points 78757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 15312 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) : 2.244075 object centre at (A) : 5.212500 9.657000 14.85900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5938642 0.5092438 midg,1,midg; midg,igrid,midg 0.2709979 0.1506716 1,midg,midg; igrid,midg,midg 0.3031798 0.7816907 gauss-seidel spectral radius is 0.9993243 estimated iterations to convergence 303 setup time was (sec) 2.260000 now iterating at: 06:13:22 rms-change max change #iterations 10.86185 387.0413 at 10iterations 6.556695 157.7324 at 20iterations 3.939642 89.29475 at 30iterations 2.356428 42.80856 at 40iterations 1.407909 25.94992 at 50iterations 0.8384481 15.96433 at 60iterations 0.4987905 9.598679 at 70iterations 0.2967761 5.446649 at 80iterations 0.1764413 3.185565 at 90iterations 0.1047571 1.971827 at 100iterations 6.2246468E-02 1.060234 at 110iterations 3.7109178E-02 0.6198425 at 120iterations 2.2259915E-02 0.3754444 at 130iterations 1.3480470E-02 0.2157898 at 140iterations 8.3462736E-03 0.1408997 at 150iterations 5.3460998E-03 9.8270416E-02 at 160iterations 3.6024200E-03 6.1323166E-02 at 170iterations 2.5778159E-03 5.0172806E-02 at 180iterations finished qdiffx linear iterations at : 06:13:32 total time elapsed so far: 11.92000 # loops : 180 mean,max change (kT/e) : 2.5778159E-03 5.0172806E-02 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 06:13:32 12.095u 0.169s 0:12.72 96.3% 0+0k 0+0io 0pf+0w