Tue Oct 11 08:08:50 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 08:08:50 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 = 2291 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: 0.6390350 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): -19.36900 25.34000 ymin,ymax (A): 21.67700 77.38600 zmin,zma (A): 2.006000 51.32500 x,y,z range (A): 44.70900 55.70900 49.31900 scale (grids/A): 0.6390350 object centre (A): 2.985500 49.53150 26.66550 number of atom coordinates read : 2291 total number of charged atoms : 2154 net assigned charge : 5.500013 assigned positive charge : 343.2724 centred at (gu) : 90.37405 87.73377 91.95936 assigned negative charge : -337.7729 centred at (gu) : 90.20959 87.79229 91.90491 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6345 nv = 96 ne = 84 npr = 46479 no. pairs analyzed = 46479 no. exposed pairs = 2962 no. arc points = 20941 no. surface atoms = 990 nbur = 1301 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 3331 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2187 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4480287E-09 1.9307095E-08 midg,1,midg; midg,igrid,midg 2.1286086E-08 1.1259267E-09 1,midg,midg; igrid,midg,midg -8.2635907E-09 2.5159242E-08 gauss-seidel spectral radius is 0.9872883 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 08:08:51 rms-change max change #iterations 0.1346015 24.12419 at 10iterations 1.2782730E-02 2.048205 at 20iterations 1.3252054E-03 0.2117996 at 30iterations 1.7552087E-04 3.4469604E-02 at 40iterations 4.3417116E-05 1.0177612E-02 at 50iterations finished qdiffx linear iterations at : 08:08:55 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 4.3417116E-05 1.0177612E-02 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 08:08:55 4.401u 0.397s 0:05.08 94.2% 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 08:08:55 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 = 2291 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: 1.917105 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): -19.36900 25.34000 ymin,ymax (A): 21.67700 77.38600 zmin,zma (A): 2.006000 51.32500 x,y,z range (A): 44.70900 55.70900 49.31900 scale (grids/A): 1.917105 object centre (A): 2.985500 49.53150 26.66550 number of atom coordinates read : 2291 total number of charged atoms : 2154 net assigned charge : 5.500013 assigned positive charge : 343.2724 centred at (gu) : 91.12167 83.20109 95.87783 assigned negative charge : -337.7729 centred at (gu) : 90.62878 83.37670 95.71467 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 68524 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20941 grid for indexing accessible points = 1.400000 m= 23550 mr = 46649 m= 3478 mr = 16835 m= 222 mr = 2034 m= 3 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 232 time to turn everything in is 0.5500000 number of dielectric boundary points 30159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 16945 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) : 0.6390350 object centre at (A) : 2.985500 49.53150 26.66550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6690164E-05 3.1695798E-02 midg,1,midg; midg,igrid,midg 6.2281869E-02 2.2417799E-02 1,midg,midg; igrid,midg,midg -1.2122427E-02 2.3386907E-02 gauss-seidel spectral radius is 0.9986159 estimated iterations to convergence 213 setup time was (sec) 0.8500000 now iterating at: 08:08:56 rms-change max change #iterations 3.921685 166.2462 at 10iterations 1.821220 68.83748 at 20iterations 0.8452109 30.37332 at 30iterations 0.3933294 13.40788 at 40iterations 0.1829092 6.320541 at 50iterations 8.5122161E-02 3.049472 at 60iterations 3.9546978E-02 1.240507 at 70iterations 1.8453469E-02 0.5977783 at 80iterations 8.6285695E-03 0.2595472 at 90iterations 4.0277443E-03 0.1320095 at 100iterations 1.8945048E-03 6.1326981E-02 at 110iterations 9.0373529E-04 3.9405823E-02 at 120iterations finished qdiffx linear iterations at : 08:09:06 total time elapsed so far: 10.21000 # loops : 120 mean,max change (kT/e) : 9.0373529E-04 3.9405823E-02 energy calculations done at 10.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.37000 DelPhi exited at 08:09:06 10.380u 0.457s 0:11.33 95.5% 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 08:09:06 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 = 2291 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: 2.875658 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): -19.36900 25.34000 ymin,ymax (A): 21.67700 77.38600 zmin,zma (A): 2.006000 51.32500 x,y,z range (A): 44.70900 55.70900 49.31900 scale (grids/A): 2.875658 object centre (A): 2.985500 49.53150 26.66550 number of atom coordinates read : 2291 total number of charged atoms : 2154 net assigned charge : 5.500013 assigned positive charge : 343.2724 centred at (gu) : 91.68240 79.80145 98.81682 assigned negative charge : -337.7729 centred at (gu) : 90.94319 80.06501 98.57199 start vw surface at 0.1100000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 158138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20941 grid for indexing accessible points = 1.400000 m= 77326 mr = 113143 m= 26593 mr = 62204 m= 6008 mr = 20723 m= 991 mr = 4386 m= 83 mr = 668 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 657 time to turn everything in is 1.450000 number of dielectric boundary points 67972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 17231 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) : 1.917105 object centre at (A) : 2.985500 49.53150 26.66550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6765179E-02 0.2961363 midg,1,midg; midg,igrid,midg 0.5984128 0.5184416 1,midg,midg; igrid,midg,midg -8.8242650E-02 0.2246962 gauss-seidel spectral radius is 0.9992568 estimated iterations to convergence 289 setup time was (sec) 1.800000 now iterating at: 08:09:09 rms-change max change #iterations 9.383420 392.3941 at 10iterations 5.511387 147.7310 at 20iterations 3.214643 110.9304 at 30iterations 1.865915 43.81424 at 40iterations 1.081720 24.50554 at 50iterations 0.6248440 13.24134 at 60iterations 0.3601507 8.156729 at 70iterations 0.2078760 4.015866 at 80iterations 0.1195020 2.603481 at 90iterations 6.8770245E-02 1.325788 at 100iterations 3.9656419E-02 0.7395134 at 110iterations 2.2729902E-02 0.5022049 at 120iterations 1.3051484E-02 0.2898178 at 130iterations 7.5149294E-03 0.1427526 at 140iterations 4.3128384E-03 8.6182594E-02 at 150iterations 2.4951259E-03 4.8738480E-02 at 160iterations 1.4396716E-03 3.0546188E-02 at 170iterations 8.3948905E-04 1.6323090E-02 at 180iterations finished qdiffx linear iterations at : 08:09:27 total time elapsed so far: 19.15000 # loops : 180 mean,max change (kT/e) : 8.3948905E-04 1.6323090E-02 energy calculations done at 19.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.33000 DelPhi exited at 08:09:27 19.333u 0.689s 0:20.68 96.7% 0+0k 0+0io 0pf+0w