Sun Oct 9 06:06:22 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 Sun Oct 9 2011 at 06:06:22 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2124 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6338806 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): 11.81100 67.97300 ymin,ymax (A): -26.21700 26.72400 zmin,zma (A): -5.303000 37.19100 x,y,z range (A): 56.16200 52.94100 42.49400 scale (grids/A): 0.6338806 object centre (A): 39.89200 0.2534990 15.94400 number of atom coordinates read : 2124 total number of charged atoms : 1975 net assigned charge : -11.19398 assigned positive charge : 325.4045 centred at (gu) : 90.29875 89.45156 90.35650 assigned negative charge : -336.5989 centred at (gu) : 90.34070 89.18234 90.13406 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5860 nv = 96 ne = 84 npr = 41579 no. pairs analyzed = 41579 no. exposed pairs = 2994 no. arc points = 21396 no. surface atoms = 1006 nbur = 1118 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 274 mr = 2839 m= 4 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2800000 number of dielectric boundary points 3282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2099 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6894 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0562099E-08 5.5190696E-09 midg,1,midg; midg,igrid,midg -4.1919428E-08 7.7580236E-09 1,midg,midg; igrid,midg,midg -9.3541441E-09 -1.8226331E-08 gauss-seidel spectral radius is 0.9870775 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 06:06:22 rms-change max change #iterations 0.1280819 22.20692 at 10iterations 1.2590599E-02 1.885843 at 20iterations 1.2670415E-03 0.1992340 at 30iterations 1.6745557E-04 3.4694672E-02 at 40iterations 3.2832551E-05 7.6293945E-03 at 50iterations finished qdiffx linear iterations at : 06:06:26 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 3.2832551E-05 7.6293945E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 06:06:26 4.139u 0.241s 0:04.65 93.9% 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 06:06:26 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2124 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.901642 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): 11.81100 67.97300 ymin,ymax (A): -26.21700 26.72400 zmin,zma (A): -5.303000 37.19100 x,y,z range (A): 56.16200 52.94100 42.49400 scale (grids/A): 1.901642 object centre (A): 39.89200 0.2534990 15.94400 number of atom coordinates read : 2124 total number of charged atoms : 1975 net assigned charge : -11.19398 assigned positive charge : 325.4045 centred at (gu) : 90.89601 88.35421 91.06911 assigned negative charge : -336.5989 centred at (gu) : 91.02196 87.54700 90.40214 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 62516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21396 grid for indexing accessible points = 1.400000 m= 20598 mr = 40015 m= 2984 mr = 14298 m= 158 mr = 1662 m= 6 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 706 time to turn everything in is 0.5200000 number of dielectric boundary points 30241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15518 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) : 0.6338806 object centre at (A) : 39.89200 0.2534990 15.94400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3040751E-02 1.1046872E-03 midg,1,midg; midg,igrid,midg -6.6244155E-02 3.8870819E-02 1,midg,midg; igrid,midg,midg -5.8350965E-02 -7.4381724E-02 gauss-seidel spectral radius is 0.9985958 estimated iterations to convergence 212 setup time was (sec) 0.8300000 now iterating at: 06:06:27 rms-change max change #iterations 3.918101 188.1129 at 10iterations 1.803962 69.35999 at 20iterations 0.8345457 30.85924 at 30iterations 0.3823740 14.05486 at 40iterations 0.1778405 6.282382 at 50iterations 8.1851341E-02 2.773939 at 60iterations 3.7708253E-02 1.290465 at 70iterations 1.7534047E-02 0.5922594 at 80iterations 8.1684729E-03 0.2880173 at 90iterations 3.8382816E-03 0.1342907 at 100iterations 1.8462501E-03 7.8907013E-02 at 110iterations 9.1509678E-04 3.3954620E-02 at 120iterations finished qdiffx linear iterations at : 06:06:36 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 9.1509678E-04 3.3954620E-02 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 06:06:36 9.268u 0.272s 0:09.82 97.0% 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 Sun Oct 9 2011 at 06:06:36 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2124 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.852463 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): 11.81100 67.97300 ymin,ymax (A): -26.21700 26.72400 zmin,zma (A): -5.303000 37.19100 x,y,z range (A): 56.16200 52.94100 42.49400 scale (grids/A): 2.852463 object centre (A): 39.89200 0.2534990 15.94400 number of atom coordinates read : 2124 total number of charged atoms : 1975 net assigned charge : -11.19398 assigned positive charge : 325.4045 centred at (gu) : 91.34394 87.53132 91.60363 assigned negative charge : -336.5989 centred at (gu) : 91.53288 86.32047 90.60301 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 144411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21396 grid for indexing accessible points = 1.400000 m= 67407 mr = 97977 m= 22941 mr = 52842 m= 5052 mr = 17560 m= 698 mr = 3528 m= 35 mr = 422 m= 0 mr = 7 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 2321 time to turn everything in is 1.310000 number of dielectric boundary points 68208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 15800 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) : 1.901642 object centre at (A) : 39.89200 0.2534990 15.94400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3284728 -2.0256491E-02 midg,1,midg; midg,igrid,midg -0.8415600 0.3784772 1,midg,midg; igrid,midg,midg -1.076020 -1.259735 gauss-seidel spectral radius is 0.9992491 estimated iterations to convergence 288 setup time was (sec) 1.640000 now iterating at: 06:06:38 rms-change max change #iterations 9.312020 563.6064 at 10iterations 5.433719 134.7532 at 20iterations 3.146227 71.19719 at 30iterations 1.818050 47.17186 at 40iterations 1.043763 22.99857 at 50iterations 0.5993593 12.46718 at 60iterations 0.3436462 7.066341 at 70iterations 0.1970203 4.029211 at 80iterations 0.1127397 2.294753 at 90iterations 6.4604908E-02 1.270504 at 100iterations 3.7033889E-02 0.7298546 at 110iterations 2.1256035E-02 0.4573402 at 120iterations 1.2231058E-02 0.2492352 at 130iterations 7.0573501E-03 0.1459564 at 140iterations 4.1331928E-03 9.3185425E-02 at 150iterations 2.4791870E-03 5.8185577E-02 at 160iterations 1.5378732E-03 3.6972046E-02 at 170iterations 1.0013395E-03 2.5287628E-02 at 180iterations finished qdiffx linear iterations at : 06:06:51 total time elapsed so far: 14.72000 # loops : 180 mean,max change (kT/e) : 1.0013395E-03 2.5287628E-02 energy calculations done at 14.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.89000 DelPhi exited at 06:06:52 14.888u 0.264s 0:15.42 98.1% 0+0k 0+0io 0pf+0w