Sun Oct 9 14:09:16 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 Sun Oct 9 2011 at 14:09:16 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: VAL 225 has a net charge of -0.0260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6148426 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): -13.54900 44.35200 ymin,ymax (A): -25.07700 25.64300 zmin,zma (A): 21.99700 69.74900 x,y,z range (A): 57.90100 50.72000 47.75200 scale (grids/A): 0.6148426 object centre (A): 15.40150 0.2830000 45.87300 number of atom coordinates read : 3036 total number of charged atoms : 2644 net assigned charge : 4.974023 assigned positive charge : 421.3853 centred at (gu) : 89.42327 89.22923 89.49520 assigned negative charge : -416.4124 centred at (gu) : 89.39108 89.35524 89.36915 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6984 nv = 96 ne = 84 npr = 55804 no. pairs analyzed = 55804 no. exposed pairs = 3620 no. arc points = 25123 no. surface atoms = 1211 nbur = 1825 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 389 mr = 3634 m= 0 mr = 24 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2607 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8644 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9839146E-09 9.8617132E-09 midg,1,midg; midg,igrid,midg 1.3102152E-08 -3.6893644E-09 1,midg,midg; igrid,midg,midg 1.6070628E-09 4.7441282E-09 gauss-seidel spectral radius is 0.9863197 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 14:09:17 rms-change max change #iterations 0.1228992 20.81992 at 10iterations 1.1209290E-02 1.856741 at 20iterations 1.0287784E-03 0.1486588 at 30iterations 1.0966764E-04 1.5346527E-02 at 40iterations 2.0109526E-05 2.6807785E-03 at 50iterations finished qdiffx linear iterations at : 14:09:19 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 2.0109526E-05 2.6807785E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 14:09:19 3.081u 0.149s 0:03.54 90.9% 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 Sun Oct 9 2011 at 14:09:20 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: VAL 225 has a net charge of -0.0260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.844528 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): -13.54900 44.35200 ymin,ymax (A): -25.07700 25.64300 zmin,zma (A): 21.99700 69.74900 x,y,z range (A): 57.90100 50.72000 47.75200 scale (grids/A): 1.844528 object centre (A): 15.40150 0.2830000 45.87300 number of atom coordinates read : 3036 total number of charged atoms : 2644 net assigned charge : 4.974023 assigned positive charge : 421.3853 centred at (gu) : 88.26903 87.68725 88.48502 assigned negative charge : -416.4124 centred at (gu) : 88.17311 88.06550 88.10706 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75353 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25123 grid for indexing accessible points = 1.400000 m= 25924 mr = 51190 m= 3725 mr = 18001 m= 175 mr = 2047 m= 1 mr = 38 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 33902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 20671 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) : 0.6148426 object centre at (A) : 15.40150 0.2830000 45.87300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1148511E-02 1.7319666E-02 midg,1,midg; midg,igrid,midg 2.5994748E-02 1.3076675E-02 1,midg,midg; igrid,midg,midg -4.2592842E-02 -6.7791892E-03 gauss-seidel spectral radius is 0.9985725 estimated iterations to convergence 210 setup time was (sec) 0.7800000 now iterating at: 14:09:20 rms-change max change #iterations 4.145447 208.6416 at 10iterations 1.909167 65.93318 at 20iterations 0.8772044 31.49930 at 30iterations 0.4064752 13.00392 at 40iterations 0.1863916 6.341564 at 50iterations 8.5858978E-02 2.832939 at 60iterations 3.9493877E-02 1.366133 at 70iterations 1.8243171E-02 0.5769958 at 80iterations 8.4319422E-03 0.3108521 at 90iterations 3.9051592E-03 0.1348643 at 100iterations 1.8027793E-03 6.1504364E-02 at 110iterations 8.4154436E-04 2.7690887E-02 at 120iterations finished qdiffx linear iterations at : 14:09:26 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 8.4154436E-04 2.7690887E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 14:09:27 6.862u 0.152s 0:07.29 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 Sun Oct 9 2011 at 14:09:27 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: VAL 225 has a net charge of -0.0260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.766792 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): -13.54900 44.35200 ymin,ymax (A): -25.07700 25.64300 zmin,zma (A): 21.99700 69.74900 x,y,z range (A): 57.90100 50.72000 47.75200 scale (grids/A): 2.766792 object centre (A): 15.40150 0.2830000 45.87300 number of atom coordinates read : 3036 total number of charged atoms : 2644 net assigned charge : 4.974023 assigned positive charge : 421.3853 centred at (gu) : 87.40334 86.53063 87.72723 assigned negative charge : -416.4124 centred at (gu) : 87.25965 87.09824 87.16055 start vw surface at 0.1700000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 173857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25123 grid for indexing accessible points = 1.400000 m= 85549 mr = 124310 m= 28754 mr = 67725 m= 6376 mr = 21877 m= 803 mr = 4397 m= 40 mr = 462 m= 0 mr = 12 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.300000 number of dielectric boundary points 76596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 21150 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) : 1.844528 object centre at (A) : 15.40150 0.2830000 45.87300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1201409 0.1176356 midg,1,midg; midg,igrid,midg 0.2167367 0.1468672 1,midg,midg; igrid,midg,midg -0.7328390 -3.4924053E-02 gauss-seidel spectral radius is 0.9992466 estimated iterations to convergence 288 setup time was (sec) 1.580000 now iterating at: 14:09:29 rms-change max change #iterations 10.03976 374.5773 at 10iterations 5.942504 163.8427 at 20iterations 3.487978 80.24569 at 30iterations 2.028383 41.38934 at 40iterations 1.178373 23.87389 at 50iterations 0.6844366 16.65369 at 60iterations 0.3945780 7.449392 at 70iterations 0.2270761 4.578875 at 80iterations 0.1308173 2.754731 at 90iterations 7.5313017E-02 1.567315 at 100iterations 4.3225773E-02 0.8345852 at 110iterations 2.4769491E-02 0.4792976 at 120iterations 1.4227581E-02 0.2646446 at 130iterations 8.1620915E-03 0.1569366 at 140iterations 4.6889875E-03 8.4890366E-02 at 150iterations 2.6942883E-03 5.0590515E-02 at 160iterations 1.5540171E-03 3.0429840E-02 at 170iterations 8.9771318E-04 1.8165588E-02 at 180iterations finished qdiffx linear iterations at : 14:09:38 total time elapsed so far: 10.83000 # loops : 180 mean,max change (kT/e) : 8.9771318E-04 1.8165588E-02 energy calculations done at 10.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.99000 DelPhi exited at 14:09:38 10.994u 0.197s 0:11.54 96.8% 0+0k 0+0io 0pf+0w