Tue Oct 11 03:16:12 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 Tue Oct 11 2011 at 03:16:13 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6823584 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): -10.02700 41.11700 ymin,ymax (A): 3.401000 55.57300 zmin,zma (A): 104.8340 149.6850 x,y,z range (A): 51.14400 52.17200 44.85100 scale (grids/A): 0.6823584 object centre (A): 15.54500 29.48700 127.2595 number of atom coordinates read : 2564 total number of charged atoms : 2432 net assigned charge : 2.500013 assigned positive charge : 393.5917 centred at (gu) : 89.42253 90.98291 88.79984 assigned negative charge : -391.0926 centred at (gu) : 89.28846 91.05665 89.03767 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8150 nv = 96 ne = 84 npr = 52172 no. pairs analyzed = 52172 no. exposed pairs = 3219 no. arc points = 22474 no. surface atoms = 1090 nbur = 1474 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 530 mr = 4544 m= 4 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2077 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9265 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1699598E-07 -5.7250702E-08 midg,1,midg; midg,igrid,midg 2.9822790E-08 -1.8211777E-08 1,midg,midg; igrid,midg,midg -4.0727851E-08 5.0509968E-08 gauss-seidel spectral radius is 0.9888654 estimated iterations to convergence 77 setup time was (sec) 0.5700000 now iterating at: 03:16:13 rms-change max change #iterations 0.1898691 26.22340 at 10iterations 2.2279486E-02 2.874283 at 20iterations 2.7295579E-03 0.3313637 at 30iterations 4.0240283E-04 5.2665710E-02 at 40iterations 8.1010738E-05 1.0536194E-02 at 50iterations finished qdiffx linear iterations at : 03:16:17 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 8.1010738E-05 1.0536194E-02 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 03:16:18 4.503u 0.390s 0:05.22 93.6% 0+0k 0+0io 7pf+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 Tue Oct 11 2011 at 03:16:18 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.047075 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): -10.02700 41.11700 ymin,ymax (A): 3.401000 55.57300 zmin,zma (A): 104.8340 149.6850 x,y,z range (A): 51.14400 52.17200 44.85100 scale (grids/A): 2.047075 object centre (A): 15.54500 29.48700 127.2595 number of atom coordinates read : 2564 total number of charged atoms : 2432 net assigned charge : 2.500013 assigned positive charge : 393.5917 centred at (gu) : 88.26685 92.94817 86.39877 assigned negative charge : -391.0926 centred at (gu) : 87.86504 93.16979 87.11284 start vw surface at 0.1000000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 86390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22474 grid for indexing accessible points = 1.400000 m= 33566 mr = 59952 m= 6599 mr = 25284 m= 500 mr = 4310 m= 11 mr = 221 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 37299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19261 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) : 0.6823584 object centre at (A) : 15.54500 29.48700 127.2595 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6324098E-02 -3.8722973E-02 midg,1,midg; midg,igrid,midg 1.8374499E-02 -1.4424402E-02 1,midg,midg; igrid,midg,midg -1.7974835E-02 4.0326159E-02 gauss-seidel spectral radius is 0.9988129 estimated iterations to convergence 230 setup time was (sec) 0.9900000 now iterating at: 03:16:19 rms-change max change #iterations 4.981316 203.7995 at 10iterations 2.457901 76.02132 at 20iterations 1.217675 36.93499 at 30iterations 0.6007832 17.99602 at 40iterations 0.2973584 8.684624 at 50iterations 0.1469207 4.760315 at 60iterations 7.2368875E-02 2.181314 at 70iterations 3.5754889E-02 1.031054 at 80iterations 1.7711850E-02 0.5377973 at 90iterations 8.7905517E-03 0.2561131 at 100iterations 4.3358109E-03 0.1158867 at 110iterations 2.1442953E-03 5.8982849E-02 at 120iterations finished qdiffx linear iterations at : 03:16:30 total time elapsed so far: 11.47000 # loops : 120 mean,max change (kT/e) : 2.1442953E-03 5.8982849E-02 energy calculations done at 11.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 03:16:30 11.634u 0.477s 0:12.56 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 Tue Oct 11 2011 at 03:16:30 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.070613 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): -10.02700 41.11700 ymin,ymax (A): 3.401000 55.57300 zmin,zma (A): 104.8340 149.6850 x,y,z range (A): 51.14400 52.17200 44.85100 scale (grids/A): 3.070613 object centre (A): 15.54500 29.48700 127.2595 number of atom coordinates read : 2564 total number of charged atoms : 2432 net assigned charge : 2.500013 assigned positive charge : 393.5917 centred at (gu) : 87.40022 94.42209 84.59798 assigned negative charge : -391.0926 centred at (gu) : 86.79748 94.75471 85.66927 start vw surface at 0.1100000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 199571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22474 grid for indexing accessible points = 1.400000 m= 104765 mr = 145226 m= 42715 mr = 86066 m= 12257 mr = 35132 m= 2217 mr = 9515 m= 192 mr = 1534 m= 4 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.980000 number of dielectric boundary points 84148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 19456 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) : 2.047075 object centre at (A) : 15.54500 29.48700 127.2595 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8670238 -0.3802652 midg,1,midg; midg,igrid,midg 0.1507170 -0.2059634 1,midg,midg; igrid,midg,midg -7.8817703E-02 0.4728845 gauss-seidel spectral radius is 0.9993073 estimated iterations to convergence 300 setup time was (sec) 2.400000 now iterating at: 03:16:33 rms-change max change #iterations 11.26038 412.0144 at 10iterations 6.673047 132.2507 at 20iterations 3.941767 75.44131 at 30iterations 2.331006 40.97787 at 40iterations 1.372384 22.54174 at 50iterations 0.8083907 13.45702 at 60iterations 0.4739930 7.845136 at 70iterations 0.2788690 4.832748 at 80iterations 0.1636400 2.894024 at 90iterations 9.6103191E-02 1.633669 at 100iterations 5.6245014E-02 0.9551086 at 110iterations 3.3031017E-02 0.5872879 at 120iterations 1.9373734E-02 0.3015575 at 130iterations 1.1373934E-02 0.1831388 at 140iterations 6.6872691E-03 0.1173630 at 150iterations 3.9459569E-03 6.7434311E-02 at 160iterations 2.3400898E-03 3.8665533E-02 at 170iterations 1.3966832E-03 2.5691986E-02 at 180iterations finished qdiffx linear iterations at : 03:16:50 total time elapsed so far: 19.56000 # loops : 180 mean,max change (kT/e) : 1.3966832E-03 2.5691986E-02 energy calculations done at 19.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.72000 DelPhi exited at 03:16:51 19.722u 0.500s 0:20.53 98.4% 0+0k 0+0io 0pf+0w