Sat Oct 15 11:29:25 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 15 2011 at 11:29:25 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 = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 458 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6156187 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): -31.82300 17.49100 ymin,ymax (A): -23.23000 23.38400 zmin,zma (A): -12.55600 45.27200 x,y,z range (A): 49.31400 46.61400 57.82800 scale (grids/A): 0.6156187 object centre (A): -7.166000 7.6999664E-02 16.35800 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.58311 88.98347 89.60828 assigned negative charge : -387.4045 centred at (gu) : 88.48729 89.03067 89.48560 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6331 nv = 96 ne = 84 npr = 53900 no. pairs analyzed = 53900 no. exposed pairs = 2991 no. arc points = 21838 no. surface atoms = 1003 nbur = 1582 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 353 mr = 3533 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.2200000 number of dielectric boundary points 3126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2142 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7946 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7508251E-09 9.1122825E-09 midg,1,midg; midg,igrid,midg 7.0557640E-09 1.3968557E-10 1,midg,midg; igrid,midg,midg -3.8411594E-09 6.1612937E-09 gauss-seidel spectral radius is 0.9863322 estimated iterations to convergence 70 setup time was (sec) 0.4700000 now iterating at: 11:29:26 rms-change max change #iterations 0.1216147 22.61163 at 10iterations 1.0960362E-02 1.685513 at 20iterations 1.0277501E-03 0.1498165 at 30iterations 9.5474294E-05 1.5117645E-02 at 40iterations 9.3146937E-06 1.4495850E-03 at 50iterations finished qdiffx linear iterations at : 11:29:30 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 9.3146937E-06 1.4495850E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 11:29:31 4.135u 0.239s 0:05.63 77.4% 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 15 2011 at 11:29:31 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 = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 458 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.846856 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): -31.82300 17.49100 ymin,ymax (A): -23.23000 23.38400 zmin,zma (A): -12.55600 45.27200 x,y,z range (A): 49.31400 46.61400 57.82800 scale (grids/A): 1.846856 object centre (A): -7.166000 7.6999664E-02 16.35800 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.74889 86.95001 88.82451 assigned negative charge : -387.4045 centred at (gu) : 85.46165 87.09177 88.45663 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21838 grid for indexing accessible points = 1.400000 m= 23610 mr = 48409 m= 3213 mr = 17376 m= 138 mr = 1868 m= 0 mr = 30 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 3861 time to turn everything in is 0.3700000 number of dielectric boundary points 28699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 19269 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) : 0.6156187 object centre at (A) : -7.166000 7.6999664E-02 16.35800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9570980E-02 2.1267829E-02 midg,1,midg; midg,igrid,midg 1.3920623E-02 3.5997735E-05 1,midg,midg; igrid,midg,midg -1.0192327E-03 2.9197250E-02 gauss-seidel spectral radius is 0.9985454 estimated iterations to convergence 208 setup time was (sec) 0.6400000 now iterating at: 11:29:32 rms-change max change #iterations 3.981633 171.0256 at 10iterations 1.822542 58.13123 at 20iterations 0.8289952 30.01396 at 30iterations 0.3799223 13.27168 at 40iterations 0.1735763 5.942523 at 50iterations 7.9256505E-02 2.762530 at 60iterations 3.6302790E-02 1.194235 at 70iterations 1.6606294E-02 0.5830345 at 80iterations 7.6009757E-03 0.2570190 at 90iterations 3.4664106E-03 0.1245022 at 100iterations 1.5837833E-03 4.7683716E-02 at 110iterations 7.2742504E-04 2.6165009E-02 at 120iterations finished qdiffx linear iterations at : 11:29:48 total time elapsed so far: 9.060000 # loops : 120 mean,max change (kT/e) : 7.2742504E-04 2.6165009E-02 energy calculations done at 9.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.190000 DelPhi exited at 11:29:48 9.193u 0.312s 0:16.99 55.9% 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 Sat Oct 15 2011 at 11:29:48 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 = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 458 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.770284 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): -31.82300 17.49100 ymin,ymax (A): -23.23000 23.38400 zmin,zma (A): -12.55600 45.27200 x,y,z range (A): 49.31400 46.61400 57.82800 scale (grids/A): 2.770284 object centre (A): -7.166000 7.6999664E-02 16.35800 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.62317 85.42508 88.23649 assigned negative charge : -387.4045 centred at (gu) : 83.19235 85.63766 87.68488 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 160725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21838 grid for indexing accessible points = 1.400000 m= 78277 mr = 117158 m= 25932 mr = 64162 m= 5623 mr = 20676 m= 595 mr = 4109 m= 24 mr = 333 m= 0 mr = 6 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 12984 time to turn everything in is 0.9600000 number of dielectric boundary points 64732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 19631 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) : 1.846856 object centre at (A) : -7.166000 7.6999664E-02 16.35800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1052682 0.2258913 midg,1,midg; midg,igrid,midg 0.1589132 -1.8536408E-02 1,midg,midg; igrid,midg,midg -5.3521693E-03 0.3889138 gauss-seidel spectral radius is 0.9992282 estimated iterations to convergence 284 setup time was (sec) 1.290000 now iterating at: 11:29:51 rms-change max change #iterations 9.375235 349.7134 at 10iterations 5.395864 133.0798 at 20iterations 3.071201 91.38971 at 30iterations 1.752842 44.00533 at 40iterations 0.9992558 22.41422 at 50iterations 0.5682927 12.18185 at 60iterations 0.3234852 7.300124 at 70iterations 0.1835060 3.630392 at 80iterations 0.1039311 2.158976 at 90iterations 5.9069343E-02 1.161799 at 100iterations 3.3652972E-02 0.6242447 at 110iterations 1.9084496E-02 0.3838806 at 120iterations 1.0831942E-02 0.1924038 at 130iterations 6.1543928E-03 0.1227036 at 140iterations 3.4874177E-03 7.2773933E-02 at 150iterations 1.9837234E-03 3.8198471E-02 at 160iterations 1.1269782E-03 2.1171570E-02 at 170iterations 6.3989992E-04 1.2653351E-02 at 180iterations finished qdiffx linear iterations at : 11:30:20 total time elapsed so far: 15.88000 # loops : 180 mean,max change (kT/e) : 6.3989992E-04 1.2653351E-02 energy calculations done at 15.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.01000 DelPhi exited at 11:30:21 16.011u 0.391s 0:33.23 49.3% 0+0k 0+0io 0pf+0w