Sat Oct 8 19:08:58 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 Sat Oct 8 2011 at 19:08:58 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6243752 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): -31.93400 17.66800 ymin,ymax (A): -25.82300 21.34800 zmin,zma (A): -12.63600 44.38100 x,y,z range (A): 49.60200 47.17100 57.01700 scale (grids/A): 0.6243752 object centre (A): -7.133000 -2.237500 15.87250 number of atom coordinates read : 2599 total number of charged atoms : 2462 net assigned charge : 4.800007 assigned positive charge : 393.3700 centred at (gu) : 88.49471 89.23985 90.00726 assigned negative charge : -388.5705 centred at (gu) : 88.39226 89.28777 89.89320 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6829 nv = 96 ne = 84 npr = 52806 no. pairs analyzed = 52806 no. exposed pairs = 3125 no. arc points = 22016 no. surface atoms = 1049 nbur = 1550 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3829 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3200000 number of dielectric boundary points 3312 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2158 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8156 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1778003E-09 1.3006854E-08 midg,1,midg; midg,igrid,midg 9.5549515E-09 7.7998169E-10 1,midg,midg; igrid,midg,midg -4.7319446E-09 8.7550660E-09 gauss-seidel spectral radius is 0.9867154 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 19:08:59 rms-change max change #iterations 0.1329332 22.41453 at 10iterations 1.2563206E-02 1.909241 at 20iterations 1.1890001E-03 0.1718140 at 30iterations 1.1763469E-04 1.6471863E-02 at 40iterations 1.1908034E-05 1.8196106E-03 at 50iterations finished qdiffx linear iterations at : 19:09:02 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1908034E-05 1.8196106E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 19:09:02 3.381u 0.215s 0:03.86 93.0% 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 Sat Oct 8 2011 at 19:09:02 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.873125 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): -31.93400 17.66800 ymin,ymax (A): -25.82300 21.34800 zmin,zma (A): -12.63600 44.38100 x,y,z range (A): 49.60200 47.17100 57.01700 scale (grids/A): 1.873125 object centre (A): -7.133000 -2.237500 15.87250 number of atom coordinates read : 2599 total number of charged atoms : 2462 net assigned charge : 4.800007 assigned positive charge : 393.3700 centred at (gu) : 85.48356 87.71926 90.02119 assigned negative charge : -388.5705 centred at (gu) : 85.17646 87.86299 89.67934 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 73545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22016 grid for indexing accessible points = 1.400000 m= 27197 mr = 51580 m= 4290 mr = 20392 m= 217 mr = 2723 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2860 time to turn everything in is 0.5600000 number of dielectric boundary points 30510 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19347 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) : 0.6243752 object centre at (A) : -7.133000 -2.237500 15.87250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9693222E-02 2.8326819E-02 midg,1,midg; midg,igrid,midg 1.6536536E-02 3.0664068E-03 1,midg,midg; igrid,midg,midg -1.5964555E-04 3.6326062E-02 gauss-seidel spectral radius is 0.9985930 estimated iterations to convergence 211 setup time was (sec) 0.8300000 now iterating at: 19:09:03 rms-change max change #iterations 4.088110 169.9440 at 10iterations 1.889963 71.42557 at 20iterations 0.8776442 34.64682 at 30iterations 0.4039481 13.45406 at 40iterations 0.1881113 5.927235 at 50iterations 8.7022513E-02 2.584452 at 60iterations 4.0448271E-02 1.343149 at 70iterations 1.8712496E-02 0.6042185 at 80iterations 8.6421343E-03 0.2649298 at 90iterations 4.0076734E-03 0.1222992 at 100iterations 1.8565337E-03 5.5843353E-02 at 110iterations 8.6285861E-04 2.7156830E-02 at 120iterations finished qdiffx linear iterations at : 19:09:10 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 8.6285861E-04 2.7156830E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 19:09:10 7.487u 0.225s 0:07.98 96.4% 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 Sat Oct 8 2011 at 19:09:10 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.809688 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): -31.93400 17.66800 ymin,ymax (A): -25.82300 21.34800 zmin,zma (A): -12.63600 44.38100 x,y,z range (A): 49.60200 47.17100 57.01700 scale (grids/A): 2.809688 object centre (A): -7.133000 -2.237500 15.87250 number of atom coordinates read : 2599 total number of charged atoms : 2462 net assigned charge : 4.800007 assigned positive charge : 393.3700 centred at (gu) : 83.22519 86.57883 90.03162 assigned negative charge : -388.5705 centred at (gu) : 82.76462 86.79449 89.51900 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 169917 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22016 grid for indexing accessible points = 1.400000 m= 87745 mr = 124339 m= 32350 mr = 72786 m= 7675 mr = 26289 m= 1044 mr = 5857 m= 52 mr = 624 m= 0 mr = 9 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 9507 time to turn everything in is 1.330000 number of dielectric boundary points 68879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 19693 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) : 1.873125 object centre at (A) : -7.133000 -2.237500 15.87250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1074858 0.3025118 midg,1,midg; midg,igrid,midg 0.1988741 2.2680217E-02 1,midg,midg; igrid,midg,midg -7.5933021E-03 0.4601125 gauss-seidel spectral radius is 0.9992428 estimated iterations to convergence 287 setup time was (sec) 1.640000 now iterating at: 19:09:12 rms-change max change #iterations 9.603457 379.0247 at 10iterations 5.539566 143.4619 at 20iterations 3.188917 67.07368 at 30iterations 1.828051 38.92383 at 40iterations 1.047970 20.32863 at 50iterations 0.5983503 11.73300 at 60iterations 0.3426175 5.978615 at 70iterations 0.1958234 3.392208 at 80iterations 0.1119220 2.049640 at 90iterations 6.3908100E-02 1.191195 at 100iterations 3.6530867E-02 0.6510620 at 110iterations 2.0808086E-02 0.4033966 at 120iterations 1.1902465E-02 0.2477036 at 130iterations 6.7884042E-03 0.1277304 at 140iterations 3.8680013E-03 6.9798946E-02 at 150iterations 2.2114920E-03 3.8994789E-02 at 160iterations 1.2646456E-03 2.2907257E-02 at 170iterations 7.2420092E-04 1.3330460E-02 at 180iterations finished qdiffx linear iterations at : 19:09:23 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 7.2420092E-04 1.3330460E-02 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 19:09:23 12.182u 0.236s 0:12.68 97.8% 0+0k 0+0io 0pf+0w