Tue Oct 11 00:13:11 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 00:13:11 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 = 2744 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5939570 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): 10.21400 63.97600 ymin,ymax (A): -3.551000 56.38600 zmin,zma (A): 9.639000 52.18100 x,y,z range (A): 53.76200 59.93700 42.54200 scale (grids/A): 0.5939570 object centre (A): 37.09500 26.41750 30.91000 number of atom coordinates read : 2744 total number of charged atoms : 2600 net assigned charge : 6.500019 assigned positive charge : 415.6594 centred at (gu) : 89.13329 91.68919 90.13189 assigned negative charge : -409.1603 centred at (gu) : 89.16171 91.43060 90.27669 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6293 nv = 96 ne = 84 npr = 56099 no. pairs analyzed = 56099 no. exposed pairs = 3202 no. arc points = 22649 no. surface atoms = 1081 nbur = 1663 mkacc time = 8.9999996E-02 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 = 1.456000 m= 285 mr = 3517 m= 0 mr = 20 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 127 time to turn everything in is 0.2000000 number of dielectric boundary points 3041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2309 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4546302E-09 -2.6278397E-09 midg,1,midg; midg,igrid,midg -4.2524748E-09 1.4968451E-08 1,midg,midg; igrid,midg,midg 3.6857533E-09 1.0220205E-09 gauss-seidel spectral radius is 0.9853389 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 00:13:11 rms-change max change #iterations 0.1063722 16.65489 at 10iterations 9.4914129E-03 1.389397 at 20iterations 1.3503556E-03 0.3315315 at 30iterations 3.5858134E-04 9.6294403E-02 at 40iterations 1.0360521E-04 2.8709412E-02 at 50iterations finished qdiffx linear iterations at : 00:13:14 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.0360521E-04 2.8709412E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 00:13:15 3.379u 0.166s 0:03.87 91.2% 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 00:13:15 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 = 2744 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.781871 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): 10.21400 63.97600 ymin,ymax (A): -3.551000 56.38600 zmin,zma (A): 9.639000 52.18100 x,y,z range (A): 53.76200 59.93700 42.54200 scale (grids/A): 1.781871 object centre (A): 37.09500 26.41750 30.91000 number of atom coordinates read : 2744 total number of charged atoms : 2600 net assigned charge : 6.500019 assigned positive charge : 415.6594 centred at (gu) : 87.39918 95.06705 90.39485 assigned negative charge : -409.1603 centred at (gu) : 87.48478 94.29141 90.82993 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69137 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22649 grid for indexing accessible points = 1.400000 m= 23693 mr = 48578 m= 3031 mr = 17548 m= 90 mr = 1813 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5029 time to turn everything in is 0.3300000 number of dielectric boundary points 27999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20270 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) : 0.5939570 object centre at (A) : 37.09500 26.41750 30.91000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9691994E-02 4.9471664E-03 midg,1,midg; midg,igrid,midg -1.7823093E-02 2.3033919E-02 1,midg,midg; igrid,midg,midg -3.8039025E-03 5.4321168E-03 gauss-seidel spectral radius is 0.9984492 estimated iterations to convergence 201 setup time was (sec) 0.5400000 now iterating at: 00:13:15 rms-change max change #iterations 3.834031 174.9947 at 10iterations 1.700803 68.27692 at 20iterations 0.7562707 24.05861 at 30iterations 0.3385665 11.05029 at 40iterations 0.1513342 4.725816 at 50iterations 6.7561977E-02 2.326923 at 60iterations 3.0204605E-02 0.9704585 at 70iterations 1.3627160E-02 0.4799519 at 80iterations 6.1950786E-03 0.2290916 at 90iterations 2.8890357E-03 0.1105309 at 100iterations 1.4080292E-03 5.7228088E-02 at 110iterations 7.2264072E-04 3.1665802E-02 at 120iterations finished qdiffx linear iterations at : 00:13:22 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 7.2264072E-04 3.1665802E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 00:13:23 7.622u 0.213s 0:08.26 94.7% 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 00:13:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2744 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.672807 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): 10.21400 63.97600 ymin,ymax (A): -3.551000 56.38600 zmin,zma (A): 9.639000 52.18100 x,y,z range (A): 53.76200 59.93700 42.54200 scale (grids/A): 2.672807 object centre (A): 37.09500 26.41750 30.91000 number of atom coordinates read : 2744 total number of charged atoms : 2600 net assigned charge : 6.500019 assigned positive charge : 415.6594 centred at (gu) : 86.09859 97.60033 90.59224 assigned negative charge : -409.1603 centred at (gu) : 86.22701 96.43707 91.24487 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 160236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22649 grid for indexing accessible points = 1.400000 m= 78802 mr = 117692 m= 26000 mr = 64948 m= 5154 mr = 20782 m= 454 mr = 3744 m= 11 mr = 257 m= 0 mr = 2 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 16921 time to turn everything in is 0.8400000 number of dielectric boundary points 63232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 20790 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) : 1.781871 object centre at (A) : 37.09500 26.41750 30.91000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2183858 6.1329279E-02 midg,1,midg; midg,igrid,midg -0.3210544 -4.2818259E-02 1,midg,midg; igrid,midg,midg -0.1053323 2.6395369E-02 gauss-seidel spectral radius is 0.9992022 estimated iterations to convergence 280 setup time was (sec) 1.070000 now iterating at: 00:13:24 rms-change max change #iterations 9.207812 439.2119 at 10iterations 5.219105 133.9850 at 20iterations 2.943392 61.60411 at 30iterations 1.659229 33.80147 at 40iterations 0.9316881 19.47142 at 50iterations 0.5246108 9.970755 at 60iterations 0.2952290 6.253418 at 70iterations 0.1658786 3.055061 at 80iterations 9.3343526E-02 1.695938 at 90iterations 5.2406330E-02 1.047718 at 100iterations 2.9532969E-02 0.5618839 at 110iterations 1.6647205E-02 0.3177762 at 120iterations 9.4360905E-03 0.2018318 at 130iterations 5.3623877E-03 0.1018677 at 140iterations 3.0796363E-03 6.3987732E-02 at 150iterations 1.8075593E-03 4.2030334E-02 at 160iterations 1.0985264E-03 2.7507782E-02 at 170iterations 6.9539389E-04 1.7375946E-02 at 180iterations finished qdiffx linear iterations at : 00:13:35 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 6.9539389E-04 1.7375946E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 00:13:36 12.278u 0.201s 0:12.91 96.5% 0+0k 0+0io 0pf+0w