Mon Oct 10 17:05:30 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 Mon Oct 10 2011 at 17:05:30 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1835 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: 0.7040303 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): -26.47200 23.06300 ymin,ymax (A): -1.226000 38.29000 zmin,zma (A): 24.87100 75.43700 x,y,z range (A): 49.53500 39.51600 50.56600 scale (grids/A): 0.7040303 object centre (A): -1.704500 18.53200 50.15400 number of atom coordinates read : 1835 total number of charged atoms : 1706 net assigned charge : -4.499981 assigned positive charge : 259.5404 centred at (gu) : 88.23475 89.73244 91.60184 assigned negative charge : -264.0403 centred at (gu) : 88.30451 89.84712 91.66170 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6272 nv = 96 ne = 84 npr = 38242 no. pairs analyzed = 38242 no. exposed pairs = 2391 no. arc points = 17714 no. surface atoms = 804 nbur = 1031 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 334 mr = 3219 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2400000 number of dielectric boundary points 3341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1525 ## 118 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6887 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2693906E-09 -7.9629913E-08 midg,1,midg; midg,igrid,midg 9.2747445E-09 -7.5674251E-08 1,midg,midg; igrid,midg,midg -1.0844478E-08 -4.4255941E-08 gauss-seidel spectral radius is 0.9894736 estimated iterations to convergence 79 setup time was (sec) 0.5100000 now iterating at: 17:05:31 rms-change max change #iterations 0.1786188 24.24246 at 10iterations 2.2041181E-02 3.313400 at 20iterations 2.6232803E-03 0.4477634 at 30iterations 3.1536701E-04 4.7324181E-02 at 40iterations 3.8205253E-05 6.4233541E-03 at 50iterations finished qdiffx linear iterations at : 17:05:35 total time elapsed so far: 4.410000 # loops : 50 mean,max change (kT/e) : 3.8205253E-05 6.4233541E-03 energy calculations done at 4.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 17:05:35 4.591u 0.369s 0:05.45 90.8% 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 Mon Oct 10 2011 at 17:05:35 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1835 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: 2.112091 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): -26.47200 23.06300 ymin,ymax (A): -1.226000 38.29000 zmin,zma (A): 24.87100 75.43700 x,y,z range (A): 49.53500 39.51600 50.56600 scale (grids/A): 2.112091 object centre (A): -1.704500 18.53200 50.15400 number of atom coordinates read : 1835 total number of charged atoms : 1706 net assigned charge : -4.499981 assigned positive charge : 259.5404 centred at (gu) : 84.70441 89.19749 94.80596 assigned negative charge : -264.0403 centred at (gu) : 84.91383 89.54167 94.98534 start vw surface at 0.1000000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17714 grid for indexing accessible points = 1.400000 m= 23169 mr = 44144 m= 3940 mr = 16739 m= 325 mr = 2552 m= 13 mr = 161 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 178 time to turn everything in is 0.5400000 number of dielectric boundary points 30420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 13554 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) : 0.7040303 object centre at (A) : -1.704500 18.53200 50.15400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3294509E-02 -7.7537023E-02 midg,1,midg; midg,igrid,midg 1.6875973E-02 -1.6510010E-02 1,midg,midg; igrid,midg,midg 3.1888071E-02 2.0022510E-02 gauss-seidel spectral radius is 0.9988135 estimated iterations to convergence 230 setup time was (sec) 0.8300000 now iterating at: 17:05:37 rms-change max change #iterations 4.186182 275.8405 at 10iterations 2.045912 81.70201 at 20iterations 1.005622 34.25570 at 30iterations 0.4946381 17.66358 at 40iterations 0.2433662 8.079500 at 50iterations 0.1200646 4.062745 at 60iterations 5.9149470E-02 1.877598 at 70iterations 2.8959814E-02 0.9380970 at 80iterations 1.4282657E-02 0.4404526 at 90iterations 7.0290221E-03 0.2226448 at 100iterations 3.4703966E-03 0.1113477 at 110iterations 1.7056536E-03 5.6072235E-02 at 120iterations finished qdiffx linear iterations at : 17:05:46 total time elapsed so far: 10.29000 # loops : 120 mean,max change (kT/e) : 1.7056536E-03 5.6072235E-02 energy calculations done at 10.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.45000 DelPhi exited at 17:05:47 10.457u 0.441s 0:11.25 96.8% 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 Mon Oct 10 2011 at 17:05:47 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1835 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: 3.168137 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): -26.47200 23.06300 ymin,ymax (A): -1.226000 38.29000 zmin,zma (A): 24.87100 75.43700 x,y,z range (A): 49.53500 39.51600 50.56600 scale (grids/A): 3.168137 object centre (A): -1.704500 18.53200 50.15400 number of atom coordinates read : 1835 total number of charged atoms : 1706 net assigned charge : -4.499981 assigned positive charge : 259.5404 centred at (gu) : 82.05664 88.79644 97.20895 assigned negative charge : -264.0403 centred at (gu) : 82.37071 89.31258 97.47799 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 153790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17714 grid for indexing accessible points = 1.400000 m= 74492 mr = 107480 m= 27593 mr = 59896 m= 7259 mr = 22004 m= 1321 mr = 5551 m= 147 mr = 967 m= 8 mr = 102 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 628 time to turn everything in is 1.690000 number of dielectric boundary points 68604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 13648 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) : 2.112091 object centre at (A) : -1.704500 18.53200 50.15400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9352486 -0.7196614 midg,1,midg; midg,igrid,midg 0.1114997 -0.1164030 1,midg,midg; igrid,midg,midg 0.2839144 0.3237482 gauss-seidel spectral radius is 0.9993008 estimated iterations to convergence 298 setup time was (sec) 2.020000 now iterating at: 17:05:49 rms-change max change #iterations 9.268771 324.6639 at 10iterations 5.447067 135.5310 at 20iterations 3.204389 73.70166 at 30iterations 1.880955 43.05498 at 40iterations 1.098567 24.48728 at 50iterations 0.6446298 13.70501 at 60iterations 0.3765877 7.236695 at 70iterations 0.2201195 4.189270 at 80iterations 0.1284234 2.474688 at 90iterations 7.4812144E-02 1.481853 at 100iterations 4.3702029E-02 0.7897835 at 110iterations 2.5467444E-02 0.4372139 at 120iterations 1.4877845E-02 0.3074303 at 130iterations 8.6736456E-03 0.1530409 at 140iterations 5.0647799E-03 8.8268280E-02 at 150iterations 2.9547494E-03 5.1345825E-02 at 160iterations 1.7239645E-03 3.2451630E-02 at 170iterations 1.0103117E-03 1.9590378E-02 at 180iterations finished qdiffx linear iterations at : 17:06:06 total time elapsed so far: 18.69000 # loops : 180 mean,max change (kT/e) : 1.0103117E-03 1.9590378E-02 energy calculations done at 18.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.84000 DelPhi exited at 17:06:06 18.849u 0.483s 0:19.73 97.9% 0+0k 0+0io 0pf+0w