Sat Oct 8 20:14:21 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 20:14:21 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIR 62 has a net charge of 0.5140 !!! WARNING: GLM 90 has a net charge of -0.0940 !!! WARNING: HIR 92 has a net charge of 0.5140 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 117 has a net charge of 0.5140 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: 0.6228131 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): -31.12900 17.44100 ymin,ymax (A): -23.57300 22.54100 zmin,zma (A): -12.59600 44.56400 x,y,z range (A): 48.57000 46.11400 57.16000 scale (grids/A): 0.6228131 object centre (A): -6.844000 -0.5159998 15.98400 number of atom coordinates read : 2605 total number of charged atoms : 2461 net assigned charge : 3.962002 assigned positive charge : 396.2029 centred at (gu) : 88.52597 89.25311 89.72338 assigned negative charge : -392.2415 centred at (gu) : 88.42392 89.30859 89.61127 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6553 nv = 96 ne = 84 npr = 54637 no. pairs analyzed = 54637 no. exposed pairs = 3049 no. arc points = 21792 no. surface atoms = 1017 nbur = 1588 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 317 mr = 3626 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 141 time to turn everything in is 0.3400000 number of dielectric boundary points 3206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2162 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8120 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9685274E-09 1.0946944E-08 midg,1,midg; midg,igrid,midg 8.9462642E-09 -3.6880629E-10 1,midg,midg; igrid,midg,midg -5.5399836E-09 7.9197360E-09 gauss-seidel spectral radius is 0.9866441 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 20:14:22 rms-change max change #iterations 0.1326198 22.26167 at 10iterations 1.2232151E-02 1.875912 at 20iterations 1.1284830E-03 0.1547546 at 30iterations 1.1358748E-04 1.7864227E-02 at 40iterations 1.1929189E-05 2.1553040E-03 at 50iterations finished qdiffx linear iterations at : 20:14:25 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.1929189E-05 2.1553040E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 20:14:26 4.177u 0.271s 0:04.72 94.0% 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 20:14:26 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIR 62 has a net charge of 0.5140 !!! WARNING: GLM 90 has a net charge of -0.0940 !!! WARNING: HIR 92 has a net charge of 0.5140 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 117 has a net charge of 0.5140 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: 1.868439 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): -31.12900 17.44100 ymin,ymax (A): -23.57300 22.54100 zmin,zma (A): -12.59600 44.56400 x,y,z range (A): 48.57000 46.11400 57.16000 scale (grids/A): 1.868439 object centre (A): -6.844000 -0.5159998 15.98400 number of atom coordinates read : 2605 total number of charged atoms : 2461 net assigned charge : 3.962002 assigned positive charge : 396.2029 centred at (gu) : 85.57758 87.75881 89.16962 assigned negative charge : -392.2415 centred at (gu) : 85.27158 87.92559 88.83366 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 71039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21792 grid for indexing accessible points = 1.400000 m= 24599 mr = 49492 m= 3460 mr = 18143 m= 187 mr = 2123 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 6040 time to turn everything in is 0.6300000 number of dielectric boundary points 29471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19326 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) : 0.6228131 object centre at (A) : -6.844000 -0.5159998 15.98400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9820720E-02 2.4199052E-02 midg,1,midg; midg,igrid,midg 1.4451653E-02 1.0632680E-03 1,midg,midg; igrid,midg,midg -3.7727500E-03 3.4608927E-02 gauss-seidel spectral radius is 0.9985799 estimated iterations to convergence 210 setup time was (sec) 0.9200000 now iterating at: 20:14:27 rms-change max change #iterations 4.114281 175.6147 at 10iterations 1.899511 66.65669 at 20iterations 0.8784959 30.85100 at 30iterations 0.4045776 14.22534 at 40iterations 0.1870596 5.911351 at 50iterations 8.6214453E-02 3.032677 at 60iterations 3.9907422E-02 1.287601 at 70iterations 1.8366350E-02 0.5819244 at 80iterations 8.5077574E-03 0.2792091 at 90iterations 3.9367671E-03 0.1214943 at 100iterations 1.8179646E-03 6.1985016E-02 at 110iterations 8.3909946E-04 2.8678894E-02 at 120iterations finished qdiffx linear iterations at : 20:14:36 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 8.3909946E-04 2.8678894E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 20:14:36 9.578u 0.325s 0:10.20 96.9% 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 Sat Oct 8 2011 at 20:14:36 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIR 62 has a net charge of 0.5140 !!! WARNING: GLM 90 has a net charge of -0.0940 !!! WARNING: HIR 92 has a net charge of 0.5140 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 117 has a net charge of 0.5140 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: 2.802659 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): -31.12900 17.44100 ymin,ymax (A): -23.57300 22.54100 zmin,zma (A): -12.59600 44.56400 x,y,z range (A): 48.57000 46.11400 57.16000 scale (grids/A): 2.802659 object centre (A): -6.844000 -0.5159998 15.98400 number of atom coordinates read : 2605 total number of charged atoms : 2461 net assigned charge : 3.962002 assigned positive charge : 396.2029 centred at (gu) : 83.36621 86.63810 88.75441 assigned negative charge : -392.2415 centred at (gu) : 82.90729 86.88831 88.25040 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 164605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21792 grid for indexing accessible points = 1.400000 m= 81060 mr = 119987 m= 27528 mr = 66586 m= 6116 mr = 22067 m= 804 mr = 4506 m= 35 mr = 525 m= 0 mr = 10 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 21309 time to turn everything in is 1.590000 number of dielectric boundary points 66467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 19682 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) : 1.868439 object centre at (A) : -6.844000 -0.5159998 15.98400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1313398 0.2868311 midg,1,midg; midg,igrid,midg 0.1596501 -1.5518907E-02 1,midg,midg; igrid,midg,midg -3.8778730E-02 0.4553132 gauss-seidel spectral radius is 0.9992373 estimated iterations to convergence 286 setup time was (sec) 1.900000 now iterating at: 20:14:38 rms-change max change #iterations 9.661473 337.7503 at 10iterations 5.576304 126.7568 at 20iterations 3.202370 73.77376 at 30iterations 1.833000 34.44270 at 40iterations 1.049250 20.92555 at 50iterations 0.5985289 12.42599 at 60iterations 0.3421340 6.433697 at 70iterations 0.1948014 3.739141 at 80iterations 0.1110440 2.229433 at 90iterations 6.3324332E-02 1.228401 at 100iterations 3.6029030E-02 0.6756325 at 110iterations 2.0555535E-02 0.4006844 at 120iterations 1.1712677E-02 0.2066503 at 130iterations 6.6639944E-03 0.1200027 at 140iterations 3.8085917E-03 7.8444481E-02 at 150iterations 2.1690708E-03 3.9356351E-02 at 160iterations 1.2341482E-03 2.1418571E-02 at 170iterations 7.0451788E-04 1.3214111E-02 at 180iterations finished qdiffx linear iterations at : 20:14:52 total time elapsed so far: 15.90000 # loops : 180 mean,max change (kT/e) : 7.0451788E-04 1.3214111E-02 energy calculations done at 15.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.08000 DelPhi exited at 20:14:53 16.085u 0.340s 0:16.71 98.2% 0+0k 0+0io 0pf+0w