Tue Oct 11 02:23:39 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 Tue Oct 11 2011 at 02:23:39 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2636 !!! WARNING: GLM 47 has a net charge of -0.0940 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: 0.6661801 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): 24.01700 70.22400 ymin,ymax (A): 14.43200 67.87100 zmin,zma (A): 10.34200 58.23000 x,y,z range (A): 46.20700 53.43900 47.88800 scale (grids/A): 0.6661801 object centre (A): 47.12050 41.15150 34.28600 number of atom coordinates read : 2636 total number of charged atoms : 2497 net assigned charge : 3.406004 assigned positive charge : 403.5725 centred at (gu) : 88.82812 90.36555 89.93546 assigned negative charge : -400.1674 centred at (gu) : 88.98308 90.62923 89.88157 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7862 nv = 96 ne = 84 npr = 53879 no. pairs analyzed = 53879 no. exposed pairs = 3307 no. arc points = 22348 no. surface atoms = 1114 nbur = 1522 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 446 mr = 4434 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2085 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9152 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8555778E-09 2.2589132E-08 midg,1,midg; midg,igrid,midg 6.6042908E-08 -5.8964325E-08 1,midg,midg; igrid,midg,midg 5.9388732E-08 -2.1359133E-08 gauss-seidel spectral radius is 0.9883232 estimated iterations to convergence 76 setup time was (sec) 0.6400000 now iterating at: 02:23:40 rms-change max change #iterations 0.1757023 28.04027 at 10iterations 2.1480935E-02 2.679783 at 20iterations 4.6516606E-03 0.6814270 at 30iterations 1.7876059E-03 0.2779770 at 40iterations 7.5396168E-04 0.1170044 at 50iterations finished qdiffx linear iterations at : 02:23:43 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 7.5396168E-04 0.1170044 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 02:23:44 4.233u 0.291s 0:04.94 91.4% 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 Tue Oct 11 2011 at 02:23:44 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2636 !!! WARNING: GLM 47 has a net charge of -0.0940 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: 1.998540 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): 24.01700 70.22400 ymin,ymax (A): 14.43200 67.87100 zmin,zma (A): 10.34200 58.23000 x,y,z range (A): 46.20700 53.43900 47.88800 scale (grids/A): 1.998540 object centre (A): 47.12050 41.15150 34.28600 number of atom coordinates read : 2636 total number of charged atoms : 2497 net assigned charge : 3.406004 assigned positive charge : 403.5725 centred at (gu) : 86.48365 91.09612 89.80585 assigned negative charge : -400.1674 centred at (gu) : 86.94900 91.88747 89.64463 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 84649 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22348 grid for indexing accessible points = 1.400000 m= 31587 mr = 59627 m= 5429 mr = 23550 m= 380 mr = 3470 m= 7 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 35258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 19734 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) : 0.6661801 object centre at (A) : 47.12050 41.15150 34.28600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9642701E-02 -1.1875737E-02 midg,1,midg; midg,igrid,midg 7.0080213E-02 -6.6037834E-02 1,midg,midg; igrid,midg,midg 5.2997582E-02 -1.6004074E-02 gauss-seidel spectral radius is 0.9987605 estimated iterations to convergence 225 setup time was (sec) 1.070000 now iterating at: 02:23:45 rms-change max change #iterations 4.771063 209.3106 at 10iterations 2.325058 77.78770 at 20iterations 1.130191 34.54999 at 30iterations 0.5499809 16.57683 at 40iterations 0.2694485 7.811508 at 50iterations 0.1316710 4.121183 at 60iterations 6.4560570E-02 1.963037 at 70iterations 3.2274589E-02 0.9364271 at 80iterations 1.6567016E-02 0.5089951 at 90iterations 9.0467604E-03 0.3189812 at 100iterations 5.3667743E-03 0.1970215 at 110iterations 3.4981519E-03 0.1207657 at 120iterations finished qdiffx linear iterations at : 02:23:54 total time elapsed so far: 9.800000 # loops : 120 mean,max change (kT/e) : 3.4981519E-03 0.1207657 energy calculations done at 9.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.990000 DelPhi exited at 02:23:54 9.991u 0.324s 0:10.74 95.9% 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 Tue Oct 11 2011 at 02:23:54 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2636 !!! WARNING: GLM 47 has a net charge of -0.0940 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: 2.997810 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): 24.01700 70.22400 ymin,ymax (A): 14.43200 67.87100 zmin,zma (A): 10.34200 58.23000 x,y,z range (A): 46.20700 53.43900 47.88800 scale (grids/A): 2.997810 object centre (A): 47.12050 41.15150 34.28600 number of atom coordinates read : 2636 total number of charged atoms : 2497 net assigned charge : 3.406004 assigned positive charge : 403.5725 centred at (gu) : 84.72530 91.64395 89.70853 assigned negative charge : -400.1674 centred at (gu) : 85.42334 92.83112 89.46683 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 195408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22348 grid for indexing accessible points = 1.400000 m= 100661 mr = 144091 m= 38068 mr = 82731 m= 9943 mr = 30859 m= 1638 mr = 7516 m= 108 mr = 1086 m= 5 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.990000 number of dielectric boundary points 79501 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 19976 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) : 1.998540 object centre at (A) : 47.12050 41.15150 34.28600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3298081 -0.1932679 midg,1,midg; midg,igrid,midg 0.9663031 -0.8523763 1,midg,midg; igrid,midg,midg 0.4146705 -0.1509328 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 2.330000 now iterating at: 02:23:57 rms-change max change #iterations 10.92276 407.3394 at 10iterations 6.447706 152.6955 at 20iterations 3.802134 74.21783 at 30iterations 2.234846 46.42854 at 40iterations 1.312626 24.71548 at 50iterations 0.7687892 16.73835 at 60iterations 0.4504693 9.416946 at 70iterations 0.2634575 4.650049 at 80iterations 0.1538272 2.397408 at 90iterations 9.0215772E-02 1.634725 at 100iterations 5.2828740E-02 0.9847527 at 110iterations 3.1101964E-02 0.5546341 at 120iterations 1.8492660E-02 0.3234978 at 130iterations 1.1237221E-02 0.2374191 at 140iterations 7.1273833E-03 0.1443863 at 150iterations 4.7850050E-03 9.5779419E-02 at 160iterations 3.4670958E-03 7.5214386E-02 at 170iterations 2.6855345E-03 5.3551674E-02 at 180iterations finished qdiffx linear iterations at : 02:24:12 total time elapsed so far: 16.97000 # loops : 180 mean,max change (kT/e) : 2.6855345E-03 5.3551674E-02 energy calculations done at 16.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.16000 DelPhi exited at 02:24:12 17.157u 0.337s 0:17.76 98.4% 0+0k 0+0io 0pf+0w