Sun Oct 9 13:27:47 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 Sun Oct 9 2011 at 13:27:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2356 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: 0.6861593 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): -6.921000 44.15700 ymin,ymax (A): -14.08700 37.79600 zmin,zma (A): 1.801000 44.89000 x,y,z range (A): 51.07800 51.88300 43.08900 scale (grids/A): 0.6861593 object centre (A): 18.61800 11.85450 23.34550 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 89.75661 90.93587 90.90140 assigned negative charge : -353.8496 centred at (gu) : 89.73211 91.07258 90.98489 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7579 nv = 96 ne = 84 npr = 46771 no. pairs analyzed = 46771 no. exposed pairs = 2902 no. arc points = 20551 no. surface atoms = 976 nbur = 1380 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 4256 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1926 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8547 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3328008E-08 -6.8705885E-09 midg,1,midg; midg,igrid,midg 5.7785208E-08 -2.9593277E-08 1,midg,midg; igrid,midg,midg 1.5708482E-08 3.0332281E-08 gauss-seidel spectral radius is 0.9889652 estimated iterations to convergence 78 setup time was (sec) 0.3900000 now iterating at: 13:27:48 rms-change max change #iterations 0.1855313 24.96962 at 10iterations 2.2253994E-02 3.127549 at 20iterations 2.9757195E-03 0.4125595 at 30iterations 6.0513150E-04 0.1007729 at 40iterations 1.8029564E-04 2.9327393E-02 at 50iterations finished qdiffx linear iterations at : 13:27:51 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.8029564E-04 2.9327393E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 13:27:51 3.406u 0.162s 0:03.84 92.7% 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 Sun Oct 9 2011 at 13:27:51 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 = 2356 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: 2.058478 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): -6.921000 44.15700 ymin,ymax (A): -14.08700 37.79600 zmin,zma (A): 1.801000 44.89000 x,y,z range (A): 51.07800 51.88300 43.08900 scale (grids/A): 2.058478 object centre (A): 18.61800 11.85450 23.34550 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 89.26942 92.80703 92.70324 assigned negative charge : -353.8496 centred at (gu) : 89.19614 93.21770 92.95449 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20551 grid for indexing accessible points = 1.400000 m= 31241 mr = 56656 m= 5568 mr = 23363 m= 509 mr = 3567 m= 12 mr = 251 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 770 time to turn everything in is 0.4000000 number of dielectric boundary points 34299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 17551 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) : 0.6861593 object centre at (A) : 18.61800 11.85450 23.34550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5840945E-02 1.0086267E-02 midg,1,midg; midg,igrid,midg 1.5711226E-02 -4.7395088E-02 1,midg,midg; igrid,midg,midg 4.2372655E-02 -1.0921840E-02 gauss-seidel spectral radius is 0.9988024 estimated iterations to convergence 229 setup time was (sec) 0.6200000 now iterating at: 13:27:52 rms-change max change #iterations 4.710148 233.0885 at 10iterations 2.300562 77.04646 at 20iterations 1.132378 34.26067 at 30iterations 0.5566888 19.19649 at 40iterations 0.2733962 8.302740 at 50iterations 0.1349846 4.299210 at 60iterations 6.6328831E-02 2.076309 at 70iterations 3.2773804E-02 0.9310913 at 80iterations 1.6250743E-02 0.4650192 at 90iterations 8.1116194E-03 0.2424488 at 100iterations 4.1045817E-03 0.1411743 at 110iterations 2.1437325E-03 6.9370270E-02 at 120iterations finished qdiffx linear iterations at : 13:27:59 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.1437325E-03 6.9370270E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 13:28:00 7.944u 0.212s 0:08.46 96.3% 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 Sun Oct 9 2011 at 13:28:00 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 = 2356 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: 3.087717 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): -6.921000 44.15700 ymin,ymax (A): -14.08700 37.79600 zmin,zma (A): 1.801000 44.89000 x,y,z range (A): 51.07800 51.88300 43.08900 scale (grids/A): 3.087717 object centre (A): 18.61800 11.85450 23.34550 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 88.90408 94.21043 94.05482 assigned negative charge : -353.8496 centred at (gu) : 88.79402 94.82668 94.43182 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 186382 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20551 grid for indexing accessible points = 1.400000 m= 98768 mr = 136604 m= 38134 mr = 81440 m= 10191 mr = 31009 m= 2035 mr = 7754 m= 245 mr = 1493 m= 7 mr = 147 m= 0 mr = 2 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 2701 time to turn everything in is 1.190000 number of dielectric boundary points 77313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 17726 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) : 2.058478 object centre at (A) : 18.61800 11.85450 23.34550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4288315 -2.6505394E-02 midg,1,midg; midg,igrid,midg 0.2747235 -0.5929350 1,midg,midg; igrid,midg,midg 0.3990742 -0.4296880 gauss-seidel spectral radius is 0.9992920 estimated iterations to convergence 297 setup time was (sec) 1.430000 now iterating at: 13:28:01 rms-change max change #iterations 10.56687 441.8947 at 10iterations 6.252324 153.8416 at 20iterations 3.684743 85.10081 at 30iterations 2.162526 38.35844 at 40iterations 1.270497 22.40839 at 50iterations 0.7467605 13.57509 at 60iterations 0.4365091 7.539455 at 70iterations 0.2552073 4.349375 at 80iterations 0.1496970 2.557129 at 90iterations 8.7295987E-02 1.618877 at 100iterations 5.1046994E-02 0.8704681 at 110iterations 3.0068439E-02 0.5803785 at 120iterations 1.7716043E-02 0.3112106 at 130iterations 1.0579740E-02 0.1812840 at 140iterations 6.4479136E-03 0.1279488 at 150iterations 4.0696245E-03 8.4609985E-02 at 160iterations 2.6978953E-03 5.9888840E-02 at 170iterations 1.9029116E-03 4.2964935E-02 at 180iterations finished qdiffx linear iterations at : 13:28:13 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 1.9029116E-03 4.2964935E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 13:28:13 12.753u 0.192s 0:13.22 97.8% 0+0k 0+0io 0pf+0w