Sat Oct 15 13:03:04 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 15 2011 at 13:03:04 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 = 1367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.8973357 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): -2.028000 37.64500 ymin,ymax (A): -14.37400 21.24400 zmin,zma (A): -14.66100 23.22900 x,y,z range (A): 39.67300 35.61800 37.89000 scale (grids/A): 0.8973357 object centre (A): 17.80850 3.435000 4.284000 number of atom coordinates read : 1367 total number of charged atoms : 1252 net assigned charge : 0.5000017 assigned positive charge : 205.5293 centred at (gu) : 89.97729 90.46864 90.90747 assigned negative charge : -205.0291 centred at (gu) : 89.69193 90.39679 91.11118 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7739 nv = 96 ne = 84 npr = 28775 no. pairs analyzed = 28775 no. exposed pairs = 1676 no. arc points = 12210 no. surface atoms = 562 nbur = 805 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 786 mr = 4481 m= 12 mr = 262 m= 0 mr = 0 time to grow re-entrant surface = 5.9999995E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1300000 number of dielectric boundary points 3794 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 665 ## 63 charges are in solution ## iepsmp to db, and charging done at 0.2000000 number of grid points assigned charge 6604 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7406124E-06 -2.0110710E-06 midg,1,midg; midg,igrid,midg -4.5549859E-07 8.9335458E-07 1,midg,midg; igrid,midg,midg -2.5219074E-06 2.7247590E-06 gauss-seidel spectral radius is 0.9934360 estimated iterations to convergence 100 setup time was (sec) 0.3300000 now iterating at: 13:03:04 rms-change max change #iterations 0.4045577 57.42696 at 10iterations 7.7422895E-02 10.30835 at 20iterations 1.4517776E-02 1.781105 at 30iterations 2.7143238E-03 0.3267479 at 40iterations 5.1694049E-04 6.8897247E-02 at 50iterations finished qdiffx linear iterations at : 13:03:07 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 5.1694049E-04 6.8897247E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 13:03:08 3.377u 0.187s 0:03.99 88.9% 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 15 2011 at 13:03:08 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 = 1367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.692007 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): -2.028000 37.64500 ymin,ymax (A): -14.37400 21.24400 zmin,zma (A): -14.66100 23.22900 x,y,z range (A): 39.67300 35.61800 37.89000 scale (grids/A): 2.692007 object centre (A): 17.80850 3.435000 4.284000 number of atom coordinates read : 1367 total number of charged atoms : 1252 net assigned charge : 0.5000017 assigned positive charge : 205.5293 centred at (gu) : 89.93220 91.40607 92.72277 assigned negative charge : -205.0291 centred at (gu) : 89.07566 91.19048 93.33377 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12210 grid for indexing accessible points = 1.400000 m= 37075 mr = 55357 m= 11849 mr = 29712 m= 2344 mr = 9030 m= 195 mr = 1629 m= 9 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 300 time to turn everything in is 0.4400000 number of dielectric boundary points 34928 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10013 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) : 0.8973357 object centre at (A) : 17.80850 3.435000 4.284000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2553407E-02 1.3769805E-02 midg,1,midg; midg,igrid,midg -6.2860131E-02 -7.8475125E-02 1,midg,midg; igrid,midg,midg 2.3207812E-02 0.1055991 gauss-seidel spectral radius is 0.9991328 estimated iterations to convergence 268 setup time was (sec) 0.6500000 now iterating at: 13:03:09 rms-change max change #iterations 5.463416 228.9988 at 10iterations 3.004152 99.03687 at 20iterations 1.643430 45.19790 at 30iterations 0.8968120 28.95526 at 40iterations 0.4896909 14.39983 at 50iterations 0.2686150 7.297420 at 60iterations 0.1465935 3.749575 at 70iterations 8.0262378E-02 2.220600 at 80iterations 4.3769367E-02 1.232155 at 90iterations 2.3848644E-02 0.6396573 at 100iterations 1.3079198E-02 0.3533573 at 110iterations 7.1107647E-03 0.1787910 at 120iterations finished qdiffx linear iterations at : 13:03:16 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 7.1107647E-03 0.1787910 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 13:03:16 7.973u 0.219s 0:08.51 96.1% 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 15 2011 at 13:03:17 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 = 1367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 4.038011 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): -2.028000 37.64500 ymin,ymax (A): -14.37400 21.24400 zmin,zma (A): -14.66100 23.22900 x,y,z range (A): 39.67300 35.61800 37.89000 scale (grids/A): 4.038011 object centre (A): 17.80850 3.435000 4.284000 number of atom coordinates read : 1367 total number of charged atoms : 1252 net assigned charge : 0.5000017 assigned positive charge : 205.5293 centred at (gu) : 89.89832 92.10925 94.08418 assigned negative charge : -205.0291 centred at (gu) : 88.61353 91.78574 95.00069 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 181452 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12210 grid for indexing accessible points = 1.400000 m= 105223 mr = 131881 m= 56633 mr = 89744 m= 24524 mr = 49212 m= 8330 mr = 20477 m= 2197 mr = 6759 m= 290 mr = 1717 m= 14 mr = 181 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 915 time to turn everything in is 1.380000 number of dielectric boundary points 78690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 10016 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) : 2.692007 object centre at (A) : 17.80850 3.435000 4.284000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5335890 0.1691183 midg,1,midg; midg,igrid,midg -0.3665600 -0.6471332 1,midg,midg; igrid,midg,midg 0.6283319 0.4107710 gauss-seidel spectral radius is 0.9993446 estimated iterations to convergence 308 setup time was (sec) 1.620000 now iterating at: 13:03:18 rms-change max change #iterations 11.00857 214.3567 at 10iterations 6.519828 121.8589 at 20iterations 3.861578 67.38960 at 30iterations 2.289452 34.52261 at 40iterations 1.359119 21.44988 at 50iterations 0.8068504 13.61463 at 60iterations 0.4790215 7.469985 at 70iterations 0.2842607 4.504973 at 80iterations 0.1683366 2.449829 at 90iterations 0.1000633 1.550598 at 100iterations 5.9374653E-02 0.8468990 at 110iterations 3.5400365E-02 0.5349369 at 120iterations 2.1191323E-02 0.3231804 at 130iterations 1.2685927E-02 0.1866150 at 140iterations 7.6844059E-03 0.1240692 at 150iterations 4.7203470E-03 7.8926086E-02 at 160iterations 2.9709185E-03 6.0146332E-02 at 170iterations 1.9364220E-03 3.8921356E-02 at 180iterations finished qdiffx linear iterations at : 13:03:30 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 1.9364220E-03 3.8921356E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 13:03:30 13.167u 0.207s 0:13.69 97.5% 0+0k 0+0io 0pf+0w