Wed Dec 21 14:23:03 PST 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 Wed Dec 21 2011 at 14:23:04 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 0.5847665 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): -35.40500 10.10700 ymin,ymax (A): 0.9900001 42.01900 zmin,zma (A): -2.044000 58.83500 x,y,z range (A): 45.51200 41.02900 60.87900 scale (grids/A): 0.5847665 object centre (A): -12.64900 21.50450 28.39550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 2.000005 assigned positive charge : 292.9259 centred at (gu) : 90.48279 89.43874 89.60493 assigned negative charge : -290.9262 centred at (gu) : 90.38644 89.58535 89.57993 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4516 nv = 96 ne = 84 npr = 40043 no. pairs analyzed = 40043 no. exposed pairs = 2456 no. arc points = 17396 no. surface atoms = 835 nbur = 1133 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 212 mr = 2444 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1810 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 5616 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7083041E-11 8.3644741E-10 midg,1,midg; midg,igrid,midg 3.3376881E-09 -1.7659653E-09 1,midg,midg; igrid,midg,midg -1.0212625E-09 2.3532527E-09 gauss-seidel spectral radius is 0.9848216 estimated iterations to convergence 67 setup time was (sec) 0.6400000 now iterating at: 14:23:05 rms-change max change #iterations 8.1128329E-02 13.24919 at 10iterations 6.4405198E-03 1.164509 at 20iterations 5.2070408E-04 9.8217010E-02 at 30iterations 4.0463052E-05 8.1787109E-03 at 40iterations 3.2342712E-06 6.2179565E-04 at 50iterations finished qdiffx linear iterations at : 14:23:12 total time elapsed so far: 6.800000 # loops : 50 mean,max change (kT/e) : 3.2342712E-06 6.2179565E-04 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.020000 DelPhi exited at 14:23:15 7.022u 0.597s 0:11.32 67.2% 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 Wed Dec 21 2011 at 14:23:15 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 1.754300 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): -35.40500 10.10700 ymin,ymax (A): 0.9900001 42.01900 zmin,zma (A): -2.044000 58.83500 x,y,z range (A): 45.51200 41.02900 60.87900 scale (grids/A): 1.754300 object centre (A): -12.64900 21.50450 28.39550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 2.000005 assigned positive charge : 292.9259 centred at (gu) : 91.44824 88.31626 88.81493 assigned negative charge : -290.9262 centred at (gu) : 91.15948 88.75614 88.73988 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 49396 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17396 grid for indexing accessible points = 1.400000 m= 17176 mr = 33689 m= 2096 mr = 12737 m= 85 mr = 1270 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 21033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 206 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 14263 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) : 0.5847665 object centre at (A) : -12.64900 21.50450 28.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7534734E-02 2.2274714E-02 midg,1,midg; midg,igrid,midg -3.8995637E-04 -9.9441987E-03 1,midg,midg; igrid,midg,midg -2.6170085E-03 -8.5880695E-04 gauss-seidel spectral radius is 0.9983168 estimated iterations to convergence 193 setup time was (sec) 0.8900000 now iterating at: 14:23:17 rms-change max change #iterations 3.096034 185.5101 at 10iterations 1.322537 71.23221 at 20iterations 0.5721058 29.07441 at 30iterations 0.2453963 9.339684 at 40iterations 0.1059435 4.779099 at 50iterations 4.5533769E-02 1.674884 at 60iterations 1.9617051E-02 0.7689524 at 70iterations 8.4234225E-03 0.3816528 at 80iterations 3.6419984E-03 0.1509800 at 90iterations 1.5690100E-03 6.1271906E-02 at 100iterations 6.7397865E-04 2.7145386E-02 at 110iterations 2.9170970E-04 1.1817932E-02 at 120iterations finished qdiffx linear iterations at : 14:23:33 total time elapsed so far: 17.06000 # loops : 120 mean,max change (kT/e) : 2.9170970E-04 1.1817932E-02 energy calculations done at 17.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.28000 DelPhi exited at 14:23:34 17.288u 0.611s 0:18.68 95.7% 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 Wed Dec 21 2011 at 14:23:34 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 2.631449 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): -35.40500 10.10700 ymin,ymax (A): 0.9900001 42.01900 zmin,zma (A): -2.044000 58.83500 x,y,z range (A): 45.51200 41.02900 60.87900 scale (grids/A): 2.631449 object centre (A): -12.64900 21.50450 28.39550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 2.000005 assigned positive charge : 292.9259 centred at (gu) : 92.17233 87.47430 88.22233 assigned negative charge : -290.9262 centred at (gu) : 91.73914 88.13421 88.10983 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 114411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17396 grid for indexing accessible points = 1.400000 m= 56878 mr = 81773 m= 19016 mr = 46773 m= 3618 mr = 15386 m= 426 mr = 2638 m= 20 mr = 300 m= 0 mr = 15 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 47484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 14680 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) : 1.754300 object centre at (A) : -12.64900 21.50450 28.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2969634 0.1736719 midg,1,midg; midg,igrid,midg -3.4918893E-02 -0.1349759 1,midg,midg; igrid,midg,midg -4.3860160E-02 -5.0082352E-02 gauss-seidel spectral radius is 0.9991464 estimated iterations to convergence 270 setup time was (sec) 1.710000 now iterating at: 14:23:36 rms-change max change #iterations 7.482786 295.6135 at 10iterations 4.163372 116.5811 at 20iterations 2.313241 63.96756 at 30iterations 1.280836 32.08652 at 40iterations 0.7049097 16.31797 at 50iterations 0.3898164 8.916412 at 60iterations 0.2138228 4.810291 at 70iterations 0.1177347 2.652620 at 80iterations 6.4929910E-02 1.589333 at 90iterations 3.5783231E-02 0.8037403 at 100iterations 1.9615272E-02 0.4474926 at 110iterations 1.0789196E-02 0.2450161 at 120iterations 5.9376904E-03 0.1422417 at 130iterations 3.2684577E-03 7.6044083E-02 at 140iterations 1.7969788E-03 4.1610718E-02 at 150iterations 9.8952372E-04 2.1000862E-02 at 160iterations 5.4495281E-04 1.3133764E-02 at 170iterations 2.9894966E-04 7.0772171E-03 at 180iterations finished qdiffx linear iterations at : 14:24:02 total time elapsed so far: 27.73000 # loops : 180 mean,max change (kT/e) : 2.9894966E-04 7.0772171E-03 energy calculations done at 27.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 27.94000 DelPhi exited at 14:24:03 27.945u 0.610s 0:28.88 98.8% 0+0k 0+0io 0pf+0w