Sun Oct 9 20:03:09 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 Sun Oct 9 2011 at 20:03:09 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5047 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5471703 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): 3.238000 68.30000 ymin,ymax (A): -9.004000 53.54800 zmin,zma (A): -1.253000 62.10000 x,y,z range (A): 65.06200 62.55200 63.35300 scale (grids/A): 0.5471703 object centre (A): 35.76900 22.27200 30.42350 number of atom coordinates read : 5047 total number of charged atoms : 4893 net assigned charge : 1.740048 assigned positive charge : 771.1763 centred at (gu) : 87.70304 89.29619 89.43015 assigned negative charge : -769.4418 centred at (gu) : 87.60235 89.32710 89.39765 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10070 nv = 96 ne = 84 npr = 100896 no. pairs analyzed = 100896 no. exposed pairs = 5938 no. arc points = 40850 no. surface atoms = 2033 nbur = 3014 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 426 mr = 5724 m= 0 mr = 42 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4128 ## 488 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 13095 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8420957E-10 4.5988749E-10 midg,1,midg; midg,igrid,midg 6.0905248E-10 -1.8900613E-10 1,midg,midg; igrid,midg,midg -1.9325443E-09 7.5435419E-10 gauss-seidel spectral radius is 0.9829329 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 20:03:09 rms-change max change #iterations 0.1041471 13.73536 at 10iterations 1.2140842E-02 1.936456 at 20iterations 4.6503823E-03 0.6958961 at 30iterations 2.1923205E-03 0.3353767 at 40iterations 1.0454862E-03 0.1610756 at 50iterations finished qdiffx linear iterations at : 20:03:12 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.0454862E-03 0.1610756 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 20:03:13 3.574u 0.175s 0:04.08 91.6% 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 Sun Oct 9 2011 at 20:03:13 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5047 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.641511 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): 3.238000 68.30000 ymin,ymax (A): -9.004000 53.54800 zmin,zma (A): -1.253000 62.10000 x,y,z range (A): 65.06200 62.55200 63.35300 scale (grids/A): 1.641511 object centre (A): 35.76900 22.27200 30.42350 number of atom coordinates read : 5047 total number of charged atoms : 4893 net assigned charge : 1.740048 assigned positive charge : 771.1763 centred at (gu) : 83.10816 87.88675 88.28880 assigned negative charge : -769.4418 centred at (gu) : 82.80704 87.98113 88.19290 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 112484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40850 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38746 mr = 81693 m= 4457 mr = 27975 m= 127 mr = 2376 m= 0 mr = 15 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 43755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 462 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 37516 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) : 0.5471703 object centre at (A) : 35.76900 22.27200 30.42350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6864301E-02 -1.2896204E-02 midg,1,midg; midg,igrid,midg 1.8231049E-02 8.9555681E-03 1,midg,midg; igrid,midg,midg -1.7957745E-02 1.9459223E-02 gauss-seidel spectral radius is 0.9984005 estimated iterations to convergence 198 setup time was (sec) 0.7500000 now iterating at: 20:03:14 rms-change max change #iterations 4.688062 179.0234 at 10iterations 2.058516 60.82761 at 20iterations 0.9092979 26.18189 at 30iterations 0.4009347 10.55877 at 40iterations 0.1781210 5.447086 at 50iterations 7.9692706E-02 2.798077 at 60iterations 3.6732495E-02 1.124924 at 70iterations 1.8039489E-02 0.5792103 at 80iterations 1.0045897E-02 0.2940216 at 90iterations 6.3857054E-03 0.2001266 at 100iterations 4.4747908E-03 0.1360168 at 110iterations 3.3063800E-03 9.9971771E-02 at 120iterations finished qdiffx linear iterations at : 20:03:21 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 3.3063800E-03 9.9971771E-02 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 20:03:22 8.291u 0.225s 0:08.79 96.8% 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 Sun Oct 9 2011 at 20:03:22 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5047 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.462267 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): 3.238000 68.30000 ymin,ymax (A): -9.004000 53.54800 zmin,zma (A): -1.253000 62.10000 x,y,z range (A): 65.06200 62.55200 63.35300 scale (grids/A): 2.462267 object centre (A): 35.76900 22.27200 30.42350 number of atom coordinates read : 5047 total number of charged atoms : 4893 net assigned charge : 1.740048 assigned positive charge : 771.1763 centred at (gu) : 79.66187 86.82975 87.43288 assigned negative charge : -769.4418 centred at (gu) : 79.21066 86.97172 87.28940 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 261569 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40850 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 131626 mr = 198410 m= 40795 mr = 107692 m= 7419 mr = 31653 m= 623 mr = 5154 m= 6 mr = 346 m= 0 mr = 0 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 98783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 39086 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) : 1.641511 object centre at (A) : 35.76900 22.27200 30.42350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4113179 -0.3234445 midg,1,midg; midg,igrid,midg 0.1613553 5.0594602E-03 1,midg,midg; igrid,midg,midg -0.4240660 0.2517875 gauss-seidel spectral radius is 0.9992432 estimated iterations to convergence 287 setup time was (sec) 1.600000 now iterating at: 20:03:23 rms-change max change #iterations 11.88568 308.5870 at 10iterations 6.972797 176.6593 at 20iterations 4.059215 88.33781 at 30iterations 2.364458 42.48162 at 40iterations 1.365273 25.23983 at 50iterations 0.7882282 13.29459 at 60iterations 0.4543267 7.621504 at 70iterations 0.2615931 4.378288 at 80iterations 0.1505318 2.517514 at 90iterations 8.6977348E-02 1.438080 at 100iterations 5.0322723E-02 0.8857574 at 110iterations 2.9489780E-02 0.5296860 at 120iterations 1.7720733E-02 0.3289375 at 130iterations 1.1099477E-02 0.2086754 at 140iterations 7.3659667E-03 0.1463089 at 150iterations 5.2680480E-03 0.1027679 at 160iterations 4.0113637E-03 7.4466705E-02 at 170iterations 3.2019631E-03 5.8284760E-02 at 180iterations finished qdiffx linear iterations at : 20:03:35 total time elapsed so far: 13.48000 # loops : 180 mean,max change (kT/e) : 3.2019631E-03 5.8284760E-02 energy calculations done at 13.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.62000 DelPhi exited at 20:03:36 13.619u 0.208s 0:14.10 97.9% 0+0k 0+0io 0pf+0w