Sat Oct 8 14:02:32 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 14:02:32 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6411988 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): -11.92700 43.59400 ymin,ymax (A): -22.53700 22.43100 zmin,zma (A): -2.948000 51.33500 x,y,z range (A): 55.52100 44.96800 54.28300 scale (grids/A): 0.6411988 object centre (A): 15.83350 -5.3000450E-02 24.19350 number of atom coordinates read : 3038 total number of charged atoms : 2891 net assigned charge : 1.4008060E-02 assigned positive charge : 455.9206 centred at (gu) : 88.79122 89.55209 90.82056 assigned negative charge : -455.9073 centred at (gu) : 88.77024 89.45006 90.72726 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8186 nv = 96 ne = 84 npr = 64660 no. pairs analyzed = 64660 no. exposed pairs = 3420 no. arc points = 24015 no. surface atoms = 1159 nbur = 1879 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4779 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2290 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 10066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1122361E-08 1.5648288E-08 midg,1,midg; midg,igrid,midg -1.6045615E-08 1.2957186E-08 1,midg,midg; igrid,midg,midg -3.8398378E-09 2.2975737E-09 gauss-seidel spectral radius is 0.9874277 estimated iterations to convergence 73 setup time was (sec) 0.8000000 now iterating at: 14:02:33 rms-change max change #iterations 0.1604235 21.27425 at 10iterations 1.6206751E-02 2.201612 at 20iterations 1.7092243E-03 0.2027092 at 30iterations 1.9586094E-04 2.9493332E-02 at 40iterations 2.6862879E-05 3.3788681E-03 at 50iterations finished qdiffx linear iterations at : 14:02:37 total time elapsed so far: 4.500000 # loops : 50 mean,max change (kT/e) : 2.6862879E-05 3.3788681E-03 energy calculations done at 4.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.720000 DelPhi exited at 14:02:37 4.722u 0.424s 0:05.42 94.8% 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 Sat Oct 8 2011 at 14:02:37 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.923596 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): -11.92700 43.59400 ymin,ymax (A): -22.53700 22.43100 zmin,zma (A): -2.948000 51.33500 x,y,z range (A): 55.52100 44.96800 54.28300 scale (grids/A): 1.923596 object centre (A): 15.83350 -5.3000450E-02 24.19350 number of atom coordinates read : 3038 total number of charged atoms : 2891 net assigned charge : 1.4008060E-02 assigned positive charge : 455.9206 centred at (gu) : 86.37344 88.65576 92.46115 assigned negative charge : -455.9073 centred at (gu) : 86.31039 88.34997 92.18127 start vw surface at 0.1600000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 89347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24015 grid for indexing accessible points = 1.400000 m= 32303 mr = 64673 m= 4876 mr = 24276 m= 285 mr = 3091 m= 4 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 512 time to turn everything in is 0.8700000 number of dielectric boundary points 34656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 22771 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) : 0.6411988 object centre at (A) : 15.83350 -5.3000450E-02 24.19350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5009297E-02 2.3046784E-02 midg,1,midg; midg,igrid,midg -6.4962227E-03 1.6382970E-02 1,midg,midg; igrid,midg,midg -3.2077301E-02 1.8466491E-02 gauss-seidel spectral radius is 0.9986933 estimated iterations to convergence 219 setup time was (sec) 1.210000 now iterating at: 14:02:39 rms-change max change #iterations 4.761699 192.7773 at 10iterations 2.280071 75.63389 at 20iterations 1.085731 33.75452 at 30iterations 0.5192389 15.47894 at 40iterations 0.2485043 7.069815 at 50iterations 0.1183612 3.895041 at 60iterations 5.6374911E-02 1.756889 at 70iterations 2.6944108E-02 0.7816849 at 80iterations 1.2863616E-02 0.3694768 at 90iterations 6.1581410E-03 0.2011862 at 100iterations 2.9317706E-03 7.9032898E-02 at 110iterations 1.4026953E-03 4.6010017E-02 at 120iterations finished qdiffx linear iterations at : 14:02:49 total time elapsed so far: 10.90000 # loops : 120 mean,max change (kT/e) : 1.4026953E-03 4.6010017E-02 energy calculations done at 10.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 14:02:49 11.122u 0.500s 0:11.92 97.4% 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 Sat Oct 8 2011 at 14:02:49 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.885395 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): -11.92700 43.59400 ymin,ymax (A): -22.53700 22.43100 zmin,zma (A): -2.948000 51.33500 x,y,z range (A): 55.52100 44.96800 54.28300 scale (grids/A): 2.885395 object centre (A): 15.83350 -5.3000450E-02 24.19350 number of atom coordinates read : 3038 total number of charged atoms : 2891 net assigned charge : 1.4008060E-02 assigned positive charge : 455.9206 centred at (gu) : 84.56001 87.98342 93.69145 assigned negative charge : -455.9073 centred at (gu) : 84.46544 87.52482 93.27191 start vw surface at 0.1600000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 207194 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24015 grid for indexing accessible points = 1.400000 m= 105885 mr = 156414 m= 37393 mr = 88182 m= 8831 mr = 30310 m= 1328 mr = 6676 m= 87 mr = 903 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 1.430000 no. cavity mid-points inaccessible to solvent = 1718 time to turn everything in is 2.340000 number of dielectric boundary points 78190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.500000 number of grid points assigned charge 23122 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) : 1.923596 object centre at (A) : 15.83350 -5.3000450E-02 24.19350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1472796 0.3253601 midg,1,midg; midg,igrid,midg -2.2283807E-02 0.1765245 1,midg,midg; igrid,midg,midg -0.5479674 0.2330199 gauss-seidel spectral radius is 0.9992759 estimated iterations to convergence 293 setup time was (sec) 2.720000 now iterating at: 14:02:52 rms-change max change #iterations 11.02237 504.9863 at 10iterations 6.484982 165.5049 at 20iterations 3.791136 72.63114 at 30iterations 2.216789 43.26171 at 40iterations 1.291269 23.56701 at 50iterations 0.7509287 14.69630 at 60iterations 0.4357947 7.478227 at 70iterations 0.2538047 4.630239 at 80iterations 0.1471524 2.373520 at 90iterations 8.5277684E-02 1.392944 at 100iterations 4.9580842E-02 0.8414764 at 110iterations 2.8699649E-02 0.4598250 at 120iterations 1.6656104E-02 0.2745113 at 130iterations 9.6858656E-03 0.1544142 at 140iterations 5.6372387E-03 9.1374397E-02 at 150iterations 3.2893214E-03 5.2552223E-02 at 160iterations 1.9354064E-03 3.1833649E-02 at 170iterations 1.1506850E-03 1.9792557E-02 at 180iterations finished qdiffx linear iterations at : 14:03:09 total time elapsed so far: 19.17000 # loops : 180 mean,max change (kT/e) : 1.1506850E-03 1.9792557E-02 energy calculations done at 19.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.39000 DelPhi exited at 14:03:09 19.394u 0.517s 0:20.18 98.6% 0+0k 0+0io 0pf+0w