Mon Oct 10 16:09:34 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 Mon Oct 10 2011 at 16:09:34 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2185 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: 0.6568508 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): -22.63100 29.18800 ymin,ymax (A): -13.75800 40.44000 zmin,zma (A): -30.19300 11.86300 x,y,z range (A): 51.81900 54.19800 42.05600 scale (grids/A): 0.6568508 object centre (A): 3.278500 13.34100 -9.164999 number of atom coordinates read : 2185 total number of charged atoms : 2046 net assigned charge : 1.500007 assigned positive charge : 322.0226 centred at (gu) : 88.67161 88.65545 89.29713 assigned negative charge : -320.5229 centred at (gu) : 88.57011 88.69254 89.12157 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6584 nv = 96 ne = 84 npr = 43501 no. pairs analyzed = 43501 no. exposed pairs = 2826 no. arc points = 20278 no. surface atoms = 951 nbur = 1234 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 417 mr = 3518 m= 4 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1802 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7448 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6724937E-08 2.5622176E-08 midg,1,midg; midg,igrid,midg 1.2495250E-08 -1.2469614E-09 1,midg,midg; igrid,midg,midg -1.5401012E-08 1.4335459E-08 gauss-seidel spectral radius is 0.9879585 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 16:09:35 rms-change max change #iterations 0.1508372 24.09142 at 10iterations 1.5888695E-02 2.117794 at 20iterations 1.8370218E-03 0.2773514 at 30iterations 3.8193696E-04 5.9667587E-02 at 40iterations 1.4968067E-04 2.4332047E-02 at 50iterations finished qdiffx linear iterations at : 16:09:39 total time elapsed so far: 4.760000 # loops : 50 mean,max change (kT/e) : 1.4968067E-04 2.4332047E-02 energy calculations done at 4.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.930000 DelPhi exited at 16:09:39 4.938u 0.443s 0:05.67 94.7% 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 Mon Oct 10 2011 at 16:09:39 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2185 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: 1.970552 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): -22.63100 29.18800 ymin,ymax (A): -13.75800 40.44000 zmin,zma (A): -30.19300 11.86300 x,y,z range (A): 51.81900 54.19800 42.05600 scale (grids/A): 1.970552 object centre (A): 3.278500 13.34100 -9.164999 number of atom coordinates read : 2185 total number of charged atoms : 2046 net assigned charge : 1.500007 assigned positive charge : 322.0226 centred at (gu) : 86.01449 85.96600 87.89120 assigned negative charge : -320.5229 centred at (gu) : 85.71028 86.07755 87.36468 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20278 grid for indexing accessible points = 1.400000 m= 26062 mr = 48208 m= 4493 mr = 18927 m= 379 mr = 2718 m= 5 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 31515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 16164 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) : 0.6568508 object centre at (A) : 3.278500 13.34100 -9.164999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8235009E-02 2.9829064E-02 midg,1,midg; midg,igrid,midg 1.5959814E-02 6.2472519E-04 1,midg,midg; igrid,midg,midg -5.5098636E-03 -8.5114185E-03 gauss-seidel spectral radius is 0.9986845 estimated iterations to convergence 218 setup time was (sec) 0.9300000 now iterating at: 16:09:41 rms-change max change #iterations 4.156131 183.0738 at 10iterations 1.975440 73.99609 at 20iterations 0.9403768 29.93315 at 30iterations 0.4486412 14.31157 at 40iterations 0.2141361 7.597404 at 50iterations 0.1017209 3.178057 at 60iterations 4.8477370E-02 1.848039 at 70iterations 2.3220865E-02 0.7707424 at 80iterations 1.1089214E-02 0.3716774 at 90iterations 5.3752614E-03 0.1746883 at 100iterations 2.6676101E-03 8.9496613E-02 at 110iterations 1.4038095E-03 5.0470352E-02 at 120iterations finished qdiffx linear iterations at : 16:09:51 total time elapsed so far: 11.55000 # loops : 120 mean,max change (kT/e) : 1.4038095E-03 5.0470352E-02 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 16:09:52 11.735u 0.488s 0:12.51 97.6% 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 Mon Oct 10 2011 at 16:09:52 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2185 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: 2.955828 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): -22.63100 29.18800 ymin,ymax (A): -13.75800 40.44000 zmin,zma (A): -30.19300 11.86300 x,y,z range (A): 51.81900 54.19800 42.05600 scale (grids/A): 2.955828 object centre (A): 3.278500 13.34100 -9.164999 number of atom coordinates read : 2185 total number of charged atoms : 2046 net assigned charge : 1.500007 assigned positive charge : 322.0226 centred at (gu) : 84.02172 83.94891 86.83679 assigned negative charge : -320.5229 centred at (gu) : 83.56545 84.11636 86.04697 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 162996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20278 grid for indexing accessible points = 1.400000 m= 83566 mr = 116870 m= 30764 mr = 67807 m= 8160 mr = 24305 m= 1414 mr = 5893 m= 115 mr = 922 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 71169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 16367 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) : 1.970552 object centre at (A) : 3.278500 13.34100 -9.164999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1691225 0.3525284 midg,1,midg; midg,igrid,midg 0.1093271 -0.1014735 1,midg,midg; igrid,midg,midg -0.1075451 -0.1453440 gauss-seidel spectral radius is 0.9992645 estimated iterations to convergence 291 setup time was (sec) 1.970000 now iterating at: 16:09:54 rms-change max change #iterations 9.416839 406.3349 at 10iterations 5.454072 120.8553 at 20iterations 3.160143 67.42355 at 30iterations 1.828700 35.10262 at 40iterations 1.054834 21.16919 at 50iterations 0.6103477 13.00038 at 60iterations 0.3511312 6.901417 at 70iterations 0.2026070 3.965515 at 80iterations 0.1170147 2.613616 at 90iterations 6.7236945E-02 1.264919 at 100iterations 3.8659431E-02 0.7380829 at 110iterations 2.2311660E-02 0.4228821 at 120iterations 1.2814199E-02 0.2377129 at 130iterations 7.3831640E-03 0.1425323 at 140iterations 4.2501302E-03 8.8579297E-02 at 150iterations 2.4511032E-03 4.8794746E-02 at 160iterations 1.4198408E-03 2.4288177E-02 at 170iterations 8.2363770E-04 1.8380880E-02 at 180iterations finished qdiffx linear iterations at : 16:10:12 total time elapsed so far: 19.72000 # loops : 180 mean,max change (kT/e) : 8.2363770E-04 1.8380880E-02 energy calculations done at 19.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.89000 DelPhi exited at 16:10:13 19.892u 0.502s 0:20.69 98.5% 0+0k 0+0io 0pf+0w