Thu Jan 19 13:32:50 PST 2012 #!/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 Thu Jan 19 2012 at 13:32:52 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7773 !!! WARNING: LYS 51 has a net charge of 0.0730 !!! WARNING: LYS 65 has a net charge of 0.1210 !!! WARNING: LYS 138 has a net charge of 0.0730 !!! WARNING: GLU 139 has a net charge of -0.2080 !!! WARNING: LYS 144 has a net charge of 0.1210 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: ARG 191 has a net charge of 0.2090 !!! WARNING: LYS 327 has a net charge of 0.1210 !!! WARNING: LYS 374 has a net charge of 0.0730 !!! WARNING: LYS 442 has a net charge of 0.0730 !!! WARNING: LYS 480 has a net charge of 0.3390 !!! WARNING: LYS 598 has a net charge of 0.1210 !!! WARNING: LYS 634 has a net charge of 0.3390 !!! WARNING: ASP 759 has a net charge of 0.4120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4319759 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): -3.211000 75.40500 ymin,ymax (A): -11.13000 57.69400 zmin,zma (A): -7.855000 74.55700 x,y,z range (A): 78.61600 68.82400 82.41200 scale (grids/A): 0.4319759 object centre (A): 36.09700 23.28200 33.35100 number of atom coordinates read : 7773 total number of charged atoms : 7493 net assigned charge : -3.112942 assigned positive charge : 1173.198 centred at (gu) : 89.55097 89.81309 89.74783 assigned negative charge : -1176.320 centred at (gu) : 89.52424 89.83685 89.61327 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8570 nv = 96 ne = 84 npr = 156582 no. pairs analyzed = 156582 no. exposed pairs = 9823 no. arc points = 66535 no. surface atoms = 3308 nbur = 4465 mkacc time = 0.2700000 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 = 1.932000 m= 240 mr = 4196 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5450 ## 1125 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 11707 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2696522E-11 9.1961022E-12 midg,1,midg; midg,igrid,midg 1.3177685E-12 -2.4409962E-12 1,midg,midg; igrid,midg,midg -3.2500519E-12 1.2832329E-12 gauss-seidel spectral radius is 0.9728630 estimated iterations to convergence 51 setup time was (sec) 0.6900000 now iterating at: 13:32:52 rms-change max change #iterations 3.4033470E-02 5.055864 at 10iterations 1.8852755E-03 0.3075657 at 20iterations 6.1246631E-04 7.6142311E-02 at 30iterations 2.5892744E-04 3.2254219E-02 at 40iterations 1.1020646E-04 1.3842583E-02 at 50iterations finished qdiffx linear iterations at : 13:32:59 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 1.1020646E-04 1.3842583E-02 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.880000 DelPhi exited at 13:33:00 3.880u 0.205s 0:08.90 45.8% 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 Thu Jan 19 2012 at 13:33:02 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7773 !!! WARNING: LYS 51 has a net charge of 0.0730 !!! WARNING: LYS 65 has a net charge of 0.1210 !!! WARNING: LYS 138 has a net charge of 0.0730 !!! WARNING: GLU 139 has a net charge of -0.2080 !!! WARNING: LYS 144 has a net charge of 0.1210 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: ARG 191 has a net charge of 0.2090 !!! WARNING: LYS 327 has a net charge of 0.1210 !!! WARNING: LYS 374 has a net charge of 0.0730 !!! WARNING: LYS 442 has a net charge of 0.0730 !!! WARNING: LYS 480 has a net charge of 0.3390 !!! WARNING: LYS 598 has a net charge of 0.1210 !!! WARNING: LYS 634 has a net charge of 0.3390 !!! WARNING: ASP 759 has a net charge of 0.4120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.295928 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): -3.211000 75.40500 ymin,ymax (A): -11.13000 57.69400 zmin,zma (A): -7.855000 74.55700 x,y,z range (A): 78.61600 68.82400 82.41200 scale (grids/A): 1.295928 object centre (A): 36.09700 23.28200 33.35100 number of atom coordinates read : 7773 total number of charged atoms : 7493 net assigned charge : -3.112942 assigned positive charge : 1173.198 centred at (gu) : 88.65209 89.43790 89.24211 assigned negative charge : -1176.320 centred at (gu) : 88.57318 89.51036 88.83977 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 102373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 66535 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 23173 mr = 69500 m= 1097 mr = 13488 m= 7 mr = 231 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 252 time to turn everything in is 0.5500000 number of dielectric boundary points 43431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1191 ## 39 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 52098 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) : 0.4319759 object centre at (A) : 36.09700 23.28200 33.35100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7228186E-02 4.5775510E-03 midg,1,midg; midg,igrid,midg 2.5566414E-04 -3.3279106E-03 1,midg,midg; igrid,midg,midg -2.3119138E-03 4.8361821E-03 gauss-seidel spectral radius is 0.9975187 estimated iterations to convergence 160 setup time was (sec) 0.8300000 now iterating at: 13:33:06 rms-change max change #iterations 3.370866 117.7921 at 10iterations 1.212093 39.64820 at 20iterations 0.4370846 13.64038 at 30iterations 0.1581877 4.894845 at 40iterations 5.7074860E-02 1.804325 at 50iterations 2.0782130E-02 0.7184391 at 60iterations 7.5912448E-03 0.2304916 at 70iterations 2.8596795E-03 9.7175598E-02 at 80iterations 1.1791064E-03 4.4844747E-02 at 90iterations 5.8976340E-04 1.9414902E-02 at 100iterations 3.6388272E-04 1.0809660E-02 at 110iterations 2.4979137E-04 6.4706802E-03 at 120iterations finished qdiffx linear iterations at : 13:33:22 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 2.4979137E-04 6.4706802E-03 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.230000 DelPhi exited at 13:33:22 9.230u 0.292s 0:20.50 46.4% 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 Thu Jan 19 2012 at 13:33:25 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7773 !!! WARNING: LYS 51 has a net charge of 0.0730 !!! WARNING: LYS 65 has a net charge of 0.1210 !!! WARNING: LYS 138 has a net charge of 0.0730 !!! WARNING: GLU 139 has a net charge of -0.2080 !!! WARNING: LYS 144 has a net charge of 0.1210 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: ARG 191 has a net charge of 0.2090 !!! WARNING: LYS 327 has a net charge of 0.1210 !!! WARNING: LYS 374 has a net charge of 0.0730 !!! WARNING: LYS 442 has a net charge of 0.0730 !!! WARNING: LYS 480 has a net charge of 0.3390 !!! WARNING: LYS 598 has a net charge of 0.1210 !!! WARNING: LYS 634 has a net charge of 0.3390 !!! WARNING: ASP 759 has a net charge of 0.4120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.943892 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): -3.211000 75.40500 ymin,ymax (A): -11.13000 57.69400 zmin,zma (A): -7.855000 74.55700 x,y,z range (A): 78.61600 68.82400 82.41200 scale (grids/A): 1.943892 object centre (A): 36.09700 23.28200 33.35100 number of atom coordinates read : 7773 total number of charged atoms : 7493 net assigned charge : -3.112942 assigned positive charge : 1173.198 centred at (gu) : 87.97799 89.15651 88.86269 assigned negative charge : -1176.320 centred at (gu) : 87.85983 89.26549 88.25966 start vw surface at 0.1900000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 240940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 66535 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 91501 mr = 173417 m= 15278 mr = 67566 m= 1129 mr = 9288 m= 17 mr = 444 m= 0 mr = 0 time to grow re-entrant surface = 0.6600001 no. cavity mid-points inaccessible to solvent = 912 time to turn everything in is 1.220000 number of dielectric boundary points 98150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 361 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 59136 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) : 1.295928 object centre at (A) : 36.09700 23.28200 33.35100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4934607 8.7479562E-02 midg,1,midg; midg,igrid,midg 1.5493782E-02 -9.0125680E-02 1,midg,midg; igrid,midg,midg -0.1530665 0.1876722 gauss-seidel spectral radius is 0.9990410 estimated iterations to convergence 255 setup time was (sec) 1.480000 now iterating at: 13:33:27 rms-change max change #iterations 10.37298 421.2581 at 10iterations 5.779822 174.8172 at 20iterations 3.183506 78.50101 at 30iterations 1.735478 38.64276 at 40iterations 0.9443306 21.20357 at 50iterations 0.5124918 13.39703 at 60iterations 0.2764533 6.656345 at 70iterations 0.1486639 3.134426 at 80iterations 7.9964451E-02 1.749850 at 90iterations 4.2940207E-02 0.8587973 at 100iterations 2.2975594E-02 0.4851608 at 110iterations 1.2322024E-02 0.2544441 at 120iterations 6.5885140E-03 0.1363640 at 130iterations 3.5253020E-03 6.7611694E-02 at 140iterations 1.8917671E-03 3.9196968E-02 at 150iterations 1.0181050E-03 2.0374298E-02 at 160iterations 5.5238453E-04 1.0402679E-02 at 170iterations 3.0489691E-04 5.9909821E-03 at 180iterations finished qdiffx linear iterations at : 13:33:53 total time elapsed so far: 14.58000 # loops : 180 mean,max change (kT/e) : 3.0489691E-04 5.9909821E-03 energy calculations done at 14.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.71000 DelPhi exited at 13:33:53 14.716u 0.226s 0:28.58 52.2% 0+0k 0+0io 0pf+0w