Sat Oct 8 13:17:18 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 8 2011 at 13:17:19 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3094 !!! WARNING: GLU 325 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 0.6230530 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): 12.51400 65.27900 ymin,ymax (A): 1.260000 56.84800 zmin,zma (A): 86.09600 143.2340 x,y,z range (A): 52.76500 55.58801 57.13799 scale (grids/A): 0.6230530 object centre (A): 38.89650 29.05400 114.6650 number of atom coordinates read : 3094 total number of charged atoms : 2947 net assigned charge : -3.042968 assigned positive charge : 463.6736 centred at (gu) : 90.14212 92.15707 91.36140 assigned negative charge : -466.7177 centred at (gu) : 89.99404 92.10465 91.33901 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8026 nv = 96 ne = 84 npr = 63383 no. pairs analyzed = 63383 no. exposed pairs = 3833 no. arc points = 26879 no. surface atoms = 1279 nbur = 1815 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 4459 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.3600000 number of dielectric boundary points 3919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2702 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9862 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5539254E-09 -1.1402652E-09 midg,1,midg; midg,igrid,midg -4.6320121E-09 2.8822933E-09 1,midg,midg; igrid,midg,midg -1.5378816E-08 1.0131346E-08 gauss-seidel spectral radius is 0.9867003 estimated iterations to convergence 71 setup time was (sec) 0.7000000 now iterating at: 13:17:20 rms-change max change #iterations 0.1411729 17.80088 at 10iterations 1.3624542E-02 1.801855 at 20iterations 2.0286124E-03 0.3454361 at 30iterations 7.6847820E-04 0.1526127 at 40iterations 3.5254809E-04 7.0829391E-02 at 50iterations finished qdiffx linear iterations at : 13:17:24 total time elapsed so far: 5.090000 # loops : 50 mean,max change (kT/e) : 3.5254809E-04 7.0829391E-02 energy calculations done at 5.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.270000 DelPhi exited at 13:17:25 5.270u 0.467s 0:06.00 95.5% 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 13:17:25 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3094 !!! WARNING: GLU 325 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 1.869159 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): 12.51400 65.27900 ymin,ymax (A): 1.260000 56.84800 zmin,zma (A): 86.09600 143.2340 x,y,z range (A): 52.76500 55.58801 57.13799 scale (grids/A): 1.869159 object centre (A): 38.89650 29.05400 114.6650 number of atom coordinates read : 3094 total number of charged atoms : 2947 net assigned charge : -3.042968 assigned positive charge : 463.6736 centred at (gu) : 90.42564 96.47045 94.08353 assigned negative charge : -466.7177 centred at (gu) : 89.98142 96.31344 94.01669 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87318 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26879 grid for indexing accessible points = 1.400000 m= 30329 mr = 61326 m= 4365 mr = 22144 m= 231 mr = 2590 m= 3 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 2829 time to turn everything in is 0.7300000 number of dielectric boundary points 36098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 23155 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) : 0.6230530 object centre at (A) : 38.89650 29.05400 114.6650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7292175E-02 1.3186820E-02 midg,1,midg; midg,igrid,midg -3.3300638E-02 -1.0483414E-02 1,midg,midg; igrid,midg,midg -2.0216906E-02 5.5828230E-03 gauss-seidel spectral radius is 0.9986299 estimated iterations to convergence 214 setup time was (sec) 1.100000 now iterating at: 13:17:26 rms-change max change #iterations 4.557153 211.0321 at 10iterations 2.126632 74.05095 at 20iterations 0.9895872 30.79027 at 30iterations 0.4635364 14.22044 at 40iterations 0.2169002 7.066076 at 50iterations 0.1016966 2.925497 at 60iterations 4.7679748E-02 1.455687 at 70iterations 2.2527095E-02 0.6682606 at 80iterations 1.0697195E-02 0.3788338 at 90iterations 5.2385284E-03 0.1692772 at 100iterations 2.7458037E-03 0.1067600 at 110iterations 1.6001799E-03 6.2177658E-02 at 120iterations finished qdiffx linear iterations at : 13:17:38 total time elapsed so far: 12.56000 # loops : 120 mean,max change (kT/e) : 1.6001799E-03 6.2177658E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 13:17:38 12.718u 0.534s 0:13.51 98.0% 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 13:17:38 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3094 !!! WARNING: GLU 325 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 2.803739 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): 12.51400 65.27900 ymin,ymax (A): 1.260000 56.84800 zmin,zma (A): 86.09600 143.2340 x,y,z range (A): 52.76500 55.58801 57.13799 scale (grids/A): 2.803739 object centre (A): 38.89650 29.05400 114.6650 number of atom coordinates read : 3094 total number of charged atoms : 2947 net assigned charge : -3.042968 assigned positive charge : 463.6736 centred at (gu) : 90.63810 99.70535 96.12499 assigned negative charge : -466.7177 centred at (gu) : 89.97210 99.47010 96.02480 start vw surface at 0.1300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 202519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26879 grid for indexing accessible points = 1.400000 m= 100376 mr = 149113 m= 34191 mr = 81931 m= 7648 mr = 27163 m= 969 mr = 5591 m= 75 mr = 599 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 9909 time to turn everything in is 1.880000 number of dielectric boundary points 81351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 23563 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) : 1.869159 object centre at (A) : 38.89650 29.05400 114.6650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1251799 2.3047836E-02 midg,1,midg; midg,igrid,midg -0.4518021 -0.1715590 1,midg,midg; igrid,midg,midg -0.1024959 -6.1047047E-02 gauss-seidel spectral radius is 0.9992717 estimated iterations to convergence 292 setup time was (sec) 2.300000 now iterating at: 13:17:41 rms-change max change #iterations 10.82337 415.9910 at 10iterations 6.384618 163.7079 at 20iterations 3.745126 75.84855 at 30iterations 2.195126 52.80918 at 40iterations 1.278193 23.62699 at 50iterations 0.7436292 13.12134 at 60iterations 0.4315834 8.122909 at 70iterations 0.2510091 4.340384 at 80iterations 0.1456782 2.725044 at 90iterations 8.4491238E-02 1.616028 at 100iterations 4.8808437E-02 0.9277630 at 110iterations 2.8312108E-02 0.4814720 at 120iterations 1.6470730E-02 0.2785220 at 130iterations 9.6237697E-03 0.1810665 at 140iterations 5.7102600E-03 0.1000233 at 150iterations 3.4674383E-03 8.0110550E-02 at 160iterations 2.2117542E-03 5.0317764E-02 at 170iterations 1.5090769E-03 3.5263062E-02 at 180iterations finished qdiffx linear iterations at : 13:18:01 total time elapsed so far: 21.90000 # loops : 180 mean,max change (kT/e) : 1.5090769E-03 3.5263062E-02 energy calculations done at 21.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.07000 DelPhi exited at 13:18:01 22.073u 0.566s 0:22.91 98.7% 0+0k 0+0io 0pf+0w