Sat Oct 8 14:12:34 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+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 8 2011 at 14:12:34 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2940 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6307583 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): -11.43400 43.32500 ymin,ymax (A): 10.28600 55.46500 zmin,zma (A): 36.04900 92.48900 x,y,z range (A): 54.75900 45.17900 56.44000 scale (grids/A): 0.6307583 object centre (A): 15.94550 32.87550 64.26900 number of atom coordinates read : 2940 total number of charged atoms : 2794 net assigned charge : -0.9999920 assigned positive charge : 439.5237 centred at (gu) : 89.27512 89.53266 92.10152 assigned negative charge : -440.5245 centred at (gu) : 89.28893 89.43157 92.06859 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7959 nv = 96 ne = 84 npr = 60587 no. pairs analyzed = 60587 no. exposed pairs = 3429 no. arc points = 23656 no. surface atoms = 1173 nbur = 1767 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 4720 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2288 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9570 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8665854E-09 3.5829539E-09 midg,1,midg; midg,igrid,midg -1.2819834E-08 8.1667499E-09 1,midg,midg; igrid,midg,midg 3.2723949E-10 -2.1798801E-09 gauss-seidel spectral radius is 0.9870077 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 14:12:35 rms-change max change #iterations 0.1511237 23.87189 at 10iterations 1.5033220E-02 2.236935 at 20iterations 1.5817737E-03 0.1887875 at 30iterations 2.3301702E-04 3.4092903E-02 at 40iterations 5.1029605E-05 8.1720352E-03 at 50iterations finished qdiffx linear iterations at : 14:12:39 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 5.1029605E-05 8.1720352E-03 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 14:12:40 4.694u 0.404s 0:05.38 94.6% 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 14:12:40 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2940 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.892275 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): -11.43400 43.32500 ymin,ymax (A): 10.28600 55.46500 zmin,zma (A): 36.04900 92.48900 x,y,z range (A): 54.75900 45.17900 56.44000 scale (grids/A): 1.892275 object centre (A): 15.94550 32.87550 64.26900 number of atom coordinates read : 2940 total number of charged atoms : 2794 net assigned charge : -0.9999920 assigned positive charge : 439.5237 centred at (gu) : 87.82482 88.59719 96.30407 assigned negative charge : -440.5245 centred at (gu) : 87.86687 88.29446 96.20576 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23656 grid for indexing accessible points = 1.400000 m= 32594 mr = 63476 m= 4788 mr = 24778 m= 245 mr = 2896 m= 5 mr = 85 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 185 time to turn everything in is 0.7000000 number of dielectric boundary points 33600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 21985 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) : 0.6307583 object centre at (A) : 15.94550 32.87550 64.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3030874E-02 -2.7332844E-03 midg,1,midg; midg,igrid,midg -5.1300763E-03 1.3846114E-02 1,midg,midg; igrid,midg,midg 7.8597758E-03 7.4751927E-03 gauss-seidel spectral radius is 0.9986476 estimated iterations to convergence 215 setup time was (sec) 1.060000 now iterating at: 14:12:41 rms-change max change #iterations 4.518247 181.2505 at 10iterations 2.125542 68.11590 at 20iterations 1.002207 35.87765 at 30iterations 0.4702146 14.19668 at 40iterations 0.2214244 6.724260 at 50iterations 0.1041865 3.456903 at 60iterations 4.9152829E-02 1.594079 at 70iterations 2.3195026E-02 0.6625080 at 80iterations 1.0922845E-02 0.3380485 at 90iterations 5.1527927E-03 0.1516171 at 100iterations 2.4421825E-03 7.2204590E-02 at 110iterations 1.1585684E-03 3.3348083E-02 at 120iterations finished qdiffx linear iterations at : 14:12:51 total time elapsed so far: 11.11000 # loops : 120 mean,max change (kT/e) : 1.1585684E-03 3.3348083E-02 energy calculations done at 11.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 14:12:52 11.283u 0.474s 0:12.04 97.5% 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 14:12:52 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2940 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.838413 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): -11.43400 43.32500 ymin,ymax (A): 10.28600 55.46500 zmin,zma (A): 36.04900 92.48900 x,y,z range (A): 54.75900 45.17900 56.44000 scale (grids/A): 2.838413 object centre (A): 15.94550 32.87550 64.26900 number of atom coordinates read : 2940 total number of charged atoms : 2794 net assigned charge : -0.9999920 assigned positive charge : 439.5237 centred at (gu) : 86.73727 87.89581 99.45610 assigned negative charge : -440.5245 centred at (gu) : 86.80019 87.44174 99.30859 start vw surface at 0.1200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 201781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23656 grid for indexing accessible points = 1.400000 m= 106548 mr = 153049 m= 38098 mr = 89419 m= 8442 mr = 30838 m= 1027 mr = 6166 m= 43 mr = 623 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 629 time to turn everything in is 1.840000 number of dielectric boundary points 75834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 22352 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) : 1.892275 object centre at (A) : 15.94550 32.87550 64.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8451909E-02 4.5011450E-02 midg,1,midg; midg,igrid,midg -2.3641601E-02 0.1690117 1,midg,midg; igrid,midg,midg 0.2113418 0.2684438 gauss-seidel spectral radius is 0.9992674 estimated iterations to convergence 292 setup time was (sec) 2.170000 now iterating at: 14:12:54 rms-change max change #iterations 10.63923 429.6171 at 10iterations 6.247829 115.1972 at 20iterations 3.645574 70.28378 at 30iterations 2.124723 40.89278 at 40iterations 1.235073 21.12757 at 50iterations 0.7172458 13.87349 at 60iterations 0.4158798 7.242042 at 70iterations 0.2404068 4.162672 at 80iterations 0.1390430 2.510711 at 90iterations 8.0336727E-02 1.437993 at 100iterations 4.6440020E-02 0.9058011 at 110iterations 2.6832417E-02 0.4585934 at 120iterations 1.5461012E-02 0.2809696 at 130iterations 8.9429803E-03 0.1444912 at 140iterations 5.1660775E-03 8.8790894E-02 at 150iterations 2.9945320E-03 5.1910400E-02 at 160iterations 1.7370547E-03 2.8132379E-02 at 170iterations 1.0135500E-03 1.7745972E-02 at 180iterations finished qdiffx linear iterations at : 14:13:11 total time elapsed so far: 18.85000 # loops : 180 mean,max change (kT/e) : 1.0135500E-03 1.7745972E-02 energy calculations done at 18.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.02000 DelPhi exited at 14:13:12 19.024u 0.529s 0:19.85 98.4% 0+0k 0+0io 0pf+0w