Tue Oct 11 06:22:07 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+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 Tue Oct 11 2011 at 06:22:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2041 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: 0.7193518 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): 2.543000 46.79300 ymin,ymax (A): 0.6530000 42.33800 zmin,zma (A): -2.585000 46.90400 x,y,z range (A): 44.25000 41.68500 49.48900 scale (grids/A): 0.7193518 object centre (A): 24.66800 21.49550 22.15950 number of atom coordinates read : 2041 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 90.32273 89.92708 90.31952 assigned negative charge : -304.2972 centred at (gu) : 90.50848 89.90820 90.36168 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7230 nv = 96 ne = 84 npr = 40781 no. pairs analyzed = 40781 no. exposed pairs = 2473 no. arc points = 16829 no. surface atoms = 845 nbur = 1196 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 498 mr = 4180 m= 6 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1647 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7963 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0402169E-07 6.1034079E-08 midg,1,midg; midg,igrid,midg 7.3263848E-08 9.4654418E-08 1,midg,midg; igrid,midg,midg 1.8651947E-07 -3.6982019E-08 gauss-seidel spectral radius is 0.9899195 estimated iterations to convergence 81 setup time was (sec) 0.5700000 now iterating at: 06:22:08 rms-change max change #iterations 0.2129144 29.13222 at 10iterations 2.7517062E-02 3.549911 at 20iterations 3.7488544E-03 0.4670639 at 30iterations 6.2639505E-04 8.0818176E-02 at 40iterations 1.5188332E-04 1.9832611E-02 at 50iterations finished qdiffx linear iterations at : 06:22:11 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.5188332E-04 1.9832611E-02 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 06:22:12 4.089u 0.271s 0:04.97 87.5% 0+0k 0+0io 6pf+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 06:22:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2041 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: 2.158055 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): 2.543000 46.79300 ymin,ymax (A): 0.6530000 42.33800 zmin,zma (A): -2.585000 46.90400 x,y,z range (A): 44.25000 41.68500 49.48900 scale (grids/A): 2.158055 object centre (A): 24.66800 21.49550 22.15950 number of atom coordinates read : 2041 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 90.96826 89.78131 90.95885 assigned negative charge : -304.2972 centred at (gu) : 91.52538 89.72465 91.08524 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 76566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16829 grid for indexing accessible points = 1.400000 m= 31014 mr = 54730 m= 6143 mr = 23670 m= 539 mr = 4070 m= 11 mr = 252 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 31551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15342 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) : 0.7193518 object centre at (A) : 24.66800 21.49550 22.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2882602E-02 6.5668322E-02 midg,1,midg; midg,igrid,midg 6.9009401E-03 2.9218588E-02 1,midg,midg; igrid,midg,midg 4.6989445E-02 1.2843773E-02 gauss-seidel spectral radius is 0.9988609 estimated iterations to convergence 234 setup time was (sec) 1.000000 now iterating at: 06:22:13 rms-change max change #iterations 4.665516 235.8702 at 10iterations 2.326039 90.70305 at 20iterations 1.171774 34.86270 at 30iterations 0.5847216 18.99692 at 40iterations 0.2939070 9.974127 at 50iterations 0.1476272 4.417976 at 60iterations 7.3906802E-02 2.314895 at 70iterations 3.7082151E-02 1.085351 at 80iterations 1.8636996E-02 0.6117232 at 90iterations 9.4409771E-03 0.2697730 at 100iterations 4.8072212E-03 0.1389771 at 110iterations 2.4713355E-03 7.3966980E-02 at 120iterations finished qdiffx linear iterations at : 06:22:22 total time elapsed so far: 9.480000 # loops : 120 mean,max change (kT/e) : 2.4713355E-03 7.3966980E-02 energy calculations done at 9.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 06:22:22 9.654u 0.328s 0:10.59 94.1% 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 06:22:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2041 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: 3.237083 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): 2.543000 46.79300 ymin,ymax (A): 0.6530000 42.33800 zmin,zma (A): -2.585000 46.90400 x,y,z range (A): 44.25000 41.68500 49.48900 scale (grids/A): 3.237083 object centre (A): 24.66800 21.49550 22.15950 number of atom coordinates read : 2041 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 91.45252 89.67197 91.43845 assigned negative charge : -304.2972 centred at (gu) : 92.28809 89.58704 91.62791 start vw surface at 0.1400000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 176384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16829 grid for indexing accessible points = 1.400000 m= 96238 mr = 131459 m= 39464 mr = 80449 m= 11628 mr = 32524 m= 2313 mr = 9024 m= 259 mr = 1612 m= 10 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.270000 number of dielectric boundary points 71065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.430000 number of grid points assigned charge 15432 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) : 2.158055 object centre at (A) : 24.66800 21.49550 22.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5160490 0.6703874 midg,1,midg; midg,igrid,midg -3.4618317E-03 0.2173796 1,midg,midg; igrid,midg,midg 0.3456825 0.2191385 gauss-seidel spectral radius is 0.9992996 estimated iterations to convergence 298 setup time was (sec) 2.600000 now iterating at: 06:22:25 rms-change max change #iterations 10.33130 425.7825 at 10iterations 6.153311 167.4142 at 20iterations 3.644212 81.44862 at 30iterations 2.151945 44.74738 at 40iterations 1.271488 24.54405 at 50iterations 0.7503260 17.98185 at 60iterations 0.4412538 8.485405 at 70iterations 0.2595977 5.164619 at 80iterations 0.1524348 2.844021 at 90iterations 8.9731514E-02 1.969032 at 100iterations 5.2811518E-02 1.096154 at 110iterations 3.1175010E-02 0.5694180 at 120iterations 1.8569257E-02 0.3353167 at 130iterations 1.1194979E-02 0.1969662 at 140iterations 6.9244858E-03 0.1274471 at 150iterations 4.4473335E-03 8.0741882E-02 at 160iterations 3.0184658E-03 5.5393219E-02 at 170iterations 2.1779137E-03 3.6666870E-02 at 180iterations finished qdiffx linear iterations at : 06:22:39 total time elapsed so far: 16.57000 # loops : 180 mean,max change (kT/e) : 2.1779137E-03 3.6666870E-02 energy calculations done at 16.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.75000 DelPhi exited at 06:22:40 16.754u 0.330s 0:17.42 98.0% 0+0k 0+0io 0pf+0w