Sat Oct 8 20:15:33 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+sph2.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 = amb2.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 20:15:33 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIR 62 has a net charge of 0.5140 !!! WARNING: GLM 90 has a net charge of -0.0940 !!! WARNING: HIR 92 has a net charge of 0.5140 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 117 has a net charge of 0.5140 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: 0.6169630 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): -31.26600 17.40000 ymin,ymax (A): -23.45400 22.66600 zmin,zma (A): -12.64000 45.06200 x,y,z range (A): 48.66600 46.12000 57.70200 scale (grids/A): 0.6169630 object centre (A): -6.933001 -0.3940001 16.21100 number of atom coordinates read : 2605 total number of charged atoms : 2461 net assigned charge : 3.962002 assigned positive charge : 396.2029 centred at (gu) : 88.57253 89.22681 89.60331 assigned negative charge : -392.2415 centred at (gu) : 88.46642 89.27129 89.49425 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6389 nv = 96 ne = 84 npr = 54691 no. pairs analyzed = 54691 no. exposed pairs = 2999 no. arc points = 21623 no. surface atoms = 1015 nbur = 1590 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 278 mr = 3518 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 0.2000000 number of dielectric boundary points 3110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2207 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8018 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1187862E-09 8.8110488E-09 midg,1,midg; midg,igrid,midg 6.7946453E-09 2.5462268E-10 1,midg,midg; igrid,midg,midg -5.0056066E-09 6.8991306E-09 gauss-seidel spectral radius is 0.9863908 estimated iterations to convergence 70 setup time was (sec) 0.3800000 now iterating at: 20:15:34 rms-change max change #iterations 0.1242946 21.21931 at 10iterations 1.1349075E-02 1.653145 at 20iterations 1.0106333E-03 0.1541367 at 30iterations 9.6847121E-05 1.3923645E-02 at 40iterations 8.8828710E-06 1.3160706E-03 at 50iterations finished qdiffx linear iterations at : 20:15:36 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 8.8828710E-06 1.3160706E-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) 3.340000 DelPhi exited at 20:15:37 3.341u 0.171s 0:03.78 92.8% 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 Sat Oct 8 2011 at 20:15:37 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIR 62 has a net charge of 0.5140 !!! WARNING: GLM 90 has a net charge of -0.0940 !!! WARNING: HIR 92 has a net charge of 0.5140 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 117 has a net charge of 0.5140 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: 1.850889 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): -31.26600 17.40000 ymin,ymax (A): -23.45400 22.66600 zmin,zma (A): -12.64000 45.06200 x,y,z range (A): 48.66600 46.12000 57.70200 scale (grids/A): 1.850889 object centre (A): -6.933001 -0.3940001 16.21100 number of atom coordinates read : 2605 total number of charged atoms : 2461 net assigned charge : 3.962002 assigned positive charge : 396.2029 centred at (gu) : 85.71731 87.67989 88.80953 assigned negative charge : -392.2415 centred at (gu) : 85.39899 87.81351 88.48254 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21623 grid for indexing accessible points = 1.400000 m= 23596 mr = 48514 m= 3281 mr = 17370 m= 145 mr = 2003 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 3986 time to turn everything in is 0.3300000 number of dielectric boundary points 28691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 19315 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) : 0.6169630 object centre at (A) : -6.933001 -0.3940001 16.21100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8111723E-02 2.8141269E-02 midg,1,midg; midg,igrid,midg 1.0754985E-02 1.2912164E-03 1,midg,midg; igrid,midg,midg -3.9323596E-03 3.1263709E-02 gauss-seidel spectral radius is 0.9985513 estimated iterations to convergence 208 setup time was (sec) 0.5400000 now iterating at: 20:15:38 rms-change max change #iterations 4.005828 153.3130 at 10iterations 1.837780 61.67984 at 20iterations 0.8393731 28.88678 at 30iterations 0.3851268 11.76012 at 40iterations 0.1762669 6.144491 at 50iterations 8.0871083E-02 2.624006 at 60iterations 3.6987498E-02 1.192482 at 70iterations 1.6940881E-02 0.5597992 at 80iterations 7.7514783E-03 0.2650038 at 90iterations 3.5659501E-03 0.1241055 at 100iterations 1.6270665E-03 5.8261871E-02 at 110iterations 7.4633490E-04 2.4651527E-02 at 120iterations finished qdiffx linear iterations at : 20:15:45 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 7.4633490E-04 2.4651527E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 20:15:45 7.635u 0.201s 0:08.10 96.6% 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 Sat Oct 8 2011 at 20:15:45 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIR 62 has a net charge of 0.5140 !!! WARNING: GLM 90 has a net charge of -0.0940 !!! WARNING: HIR 92 has a net charge of 0.5140 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 117 has a net charge of 0.5140 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: 2.776334 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): -31.26600 17.40000 ymin,ymax (A): -23.45400 22.66600 zmin,zma (A): -12.64000 45.06200 x,y,z range (A): 48.66600 46.12000 57.70200 scale (grids/A): 2.776334 object centre (A): -6.933001 -0.3940001 16.21100 number of atom coordinates read : 2605 total number of charged atoms : 2461 net assigned charge : 3.962002 assigned positive charge : 396.2029 centred at (gu) : 83.57586 86.51984 88.21424 assigned negative charge : -392.2415 centred at (gu) : 83.09846 86.72032 87.72379 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21623 grid for indexing accessible points = 1.400000 m= 78391 mr = 117818 m= 26234 mr = 64329 m= 5617 mr = 20966 m= 683 mr = 4124 m= 33 mr = 441 m= 0 mr = 9 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 13325 time to turn everything in is 0.8400000 number of dielectric boundary points 64650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 19688 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) : 1.850889 object centre at (A) : -6.933001 -0.3940001 16.21100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1349127 0.3684358 midg,1,midg; midg,igrid,midg 0.1245715 -5.7437900E-03 1,midg,midg; igrid,midg,midg -3.9591052E-02 0.4299603 gauss-seidel spectral radius is 0.9992277 estimated iterations to convergence 284 setup time was (sec) 1.060000 now iterating at: 20:15:46 rms-change max change #iterations 9.514569 346.6698 at 10iterations 5.454739 127.6195 at 20iterations 3.112716 81.22795 at 30iterations 1.773694 37.86759 at 40iterations 1.007887 20.73345 at 50iterations 0.5735039 10.78600 at 60iterations 0.3259832 6.365444 at 70iterations 0.1849950 3.736403 at 80iterations 0.1051097 2.038834 at 90iterations 5.9775803E-02 1.086696 at 100iterations 3.3882778E-02 0.7015495 at 110iterations 1.9265808E-02 0.3671827 at 120iterations 1.0899631E-02 0.2044554 at 130iterations 6.2055853E-03 0.1147900 at 140iterations 3.5178419E-03 6.8374634E-02 at 150iterations 1.9976655E-03 3.6907196E-02 at 160iterations 1.1341969E-03 2.0433426E-02 at 170iterations 6.4496818E-04 1.1532724E-02 at 180iterations finished qdiffx linear iterations at : 20:15:57 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 6.4496818E-04 1.1532724E-02 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 20:15:58 12.243u 0.215s 0:12.74 97.7% 0+0k 0+0io 0pf+0w