Sun Oct 9 06:01:54 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 Sun Oct 9 2011 at 06:01:54 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: 221 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 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: 0.6893747 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): 15.64900 67.29000 ymin,ymax (A): 26.72900 77.63700 zmin,zma (A): 47.73500 89.16800 x,y,z range (A): 51.64100 50.90800 41.43300 scale (grids/A): 0.6893747 object centre (A): 41.46950 52.18300 68.45150 number of atom coordinates read : 1747 total number of charged atoms : 1606 net assigned charge : -5.999990 assigned positive charge : 264.0792 centred at (gu) : 90.69703 91.42572 90.59171 assigned negative charge : -270.0792 centred at (gu) : 90.80031 91.88344 90.67336 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5673 nv = 96 ne = 84 npr = 35855 no. pairs analyzed = 35855 no. exposed pairs = 2255 no. arc points = 15844 no. surface atoms = 756 nbur = 991 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3100 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2500000 number of dielectric boundary points 2861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1464 ## 133 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6380 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.3729448E-09 -5.9547908E-08 midg,1,midg; midg,igrid,midg 6.9594655E-08 -2.2075481E-07 1,midg,midg; igrid,midg,midg -1.0833154E-09 -6.7973680E-08 gauss-seidel spectral radius is 0.9890122 estimated iterations to convergence 78 setup time was (sec) 0.4700000 now iterating at: 06:01:54 rms-change max change #iterations 0.1641710 29.11731 at 10iterations 1.9186711E-02 2.908251 at 20iterations 2.1987215E-03 0.3321875 at 30iterations 2.5217637E-04 3.7940979E-02 at 40iterations 2.9513401E-05 4.3640137E-03 at 50iterations finished qdiffx linear iterations at : 06:01:57 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 2.9513401E-05 4.3640137E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:01:58 3.310u 0.162s 0:03.83 90.6% 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 Sun Oct 9 2011 at 06:01:58 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: 221 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 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: 2.068124 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): 15.64900 67.29000 ymin,ymax (A): 26.72900 77.63700 zmin,zma (A): 47.73500 89.16800 x,y,z range (A): 51.64100 50.90800 41.43300 scale (grids/A): 2.068124 object centre (A): 41.46950 52.18300 68.45150 number of atom coordinates read : 1747 total number of charged atoms : 1606 net assigned charge : -5.999990 assigned positive charge : 264.0792 centred at (gu) : 92.09140 94.27711 91.77502 assigned negative charge : -270.0792 centred at (gu) : 92.40115 95.65033 92.02026 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 60055 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15844 grid for indexing accessible points = 1.400000 m= 22957 mr = 40679 m= 4427 mr = 17453 m= 385 mr = 3041 m= 13 mr = 224 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 762 time to turn everything in is 0.5000000 number of dielectric boundary points 26437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12750 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) : 0.6893747 object centre at (A) : 41.46950 52.18300 68.45150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0126074E-03 -3.5312600E-02 midg,1,midg; midg,igrid,midg 6.7855142E-02 -7.3771492E-02 1,midg,midg; igrid,midg,midg -2.3566669E-02 -5.6600641E-02 gauss-seidel spectral radius is 0.9987468 estimated iterations to convergence 224 setup time was (sec) 0.8100000 now iterating at: 06:01:59 rms-change max change #iterations 4.078376 200.7503 at 10iterations 1.971606 72.93121 at 20iterations 0.9511970 35.66982 at 30iterations 0.4603665 14.58453 at 40iterations 0.2216724 7.211695 at 50iterations 0.1071749 3.927639 at 60iterations 5.1845454E-02 1.774318 at 70iterations 2.5101675E-02 0.8368832 at 80iterations 1.2136482E-02 0.4395514 at 90iterations 5.8592251E-03 0.2184525 at 100iterations 2.8331778E-03 9.1394424E-02 at 110iterations 1.3660899E-03 4.7878981E-02 at 120iterations finished qdiffx linear iterations at : 06:02:06 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 1.3660899E-03 4.7878981E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 06:02:06 7.955u 0.221s 0:08.43 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 Sun Oct 9 2011 at 06:02:06 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: 221 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 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: 3.102186 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): 15.64900 67.29000 ymin,ymax (A): 26.72900 77.63700 zmin,zma (A): 47.73500 89.16800 x,y,z range (A): 51.64100 50.90800 41.43300 scale (grids/A): 3.102186 object centre (A): 41.46950 52.18300 68.45150 number of atom coordinates read : 1747 total number of charged atoms : 1606 net assigned charge : -5.999990 assigned positive charge : 264.0792 centred at (gu) : 93.13718 96.41582 92.66263 assigned negative charge : -270.0792 centred at (gu) : 93.60172 98.47552 93.03053 start vw surface at 0.1400000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 138584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15844 grid for indexing accessible points = 1.400000 m= 71521 mr = 98498 m= 29194 mr = 59128 m= 8341 mr = 24242 m= 1564 mr = 6605 m= 205 mr = 1194 m= 12 mr = 151 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 2481 time to turn everything in is 1.530000 number of dielectric boundary points 59599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 12848 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) : 2.068124 object centre at (A) : 41.46950 52.18300 68.45150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1920346 -0.2615404 midg,1,midg; midg,igrid,midg 0.6289996 -0.5266489 1,midg,midg; igrid,midg,midg -0.2517907 -0.6189229 gauss-seidel spectral radius is 0.9992756 estimated iterations to convergence 293 setup time was (sec) 1.850000 now iterating at: 06:02:08 rms-change max change #iterations 9.264914 352.4794 at 10iterations 5.351772 118.6207 at 20iterations 3.109046 61.40862 at 30iterations 1.797562 40.87879 at 40iterations 1.039321 20.65163 at 50iterations 0.5996466 12.59409 at 60iterations 0.3466789 6.516731 at 70iterations 0.2001163 3.963642 at 80iterations 0.1157169 2.225475 at 90iterations 6.6704437E-02 1.281024 at 100iterations 3.8556445E-02 0.7404175 at 110iterations 2.2209426E-02 0.4312477 at 120iterations 1.2823951E-02 0.2528839 at 130iterations 7.3960293E-03 0.1473465 at 140iterations 4.2654639E-03 8.0944061E-02 at 150iterations 2.4586676E-03 4.6653748E-02 at 160iterations 1.4175667E-03 3.1095028E-02 at 170iterations 8.1972132E-04 1.6247749E-02 at 180iterations finished qdiffx linear iterations at : 06:02:20 total time elapsed so far: 13.91000 # loops : 180 mean,max change (kT/e) : 8.1972132E-04 1.6247749E-02 energy calculations done at 13.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.10000 DelPhi exited at 06:02:21 14.106u 0.231s 0:14.59 98.2% 0+0k 0+0io 0pf+0w