Wed Dec 28 11:01:56 PST 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 Wed Dec 28 2011 at 11:01:56 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 0.6478735 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): -4.966000 34.23200 ymin,ymax (A): -3.439000 49.61500 zmin,zma (A): -23.77200 31.17700 x,y,z range (A): 39.19800 53.05400 54.94900 scale (grids/A): 0.6478735 object centre (A): 14.63300 23.08800 3.702500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 291.8019 centred at (gu) : 90.42818 92.03092 90.01414 assigned negative charge : -288.4402 centred at (gu) : 90.53897 92.17674 89.93964 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5664 nv = 96 ne = 84 npr = 40436 no. pairs analyzed = 40436 no. exposed pairs = 2456 no. arc points = 17189 no. surface atoms = 833 nbur = 1133 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 270 mr = 3147 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2800000 number of dielectric boundary points 2748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1740 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4739631E-09 1.4446971E-08 midg,1,midg; midg,igrid,midg 1.4251950E-08 -1.4684691E-08 1,midg,midg; igrid,midg,midg 1.6620939E-08 -5.9866738E-09 gauss-seidel spectral radius is 0.9875985 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 11:01:57 rms-change max change #iterations 0.1344840 24.73788 at 10iterations 1.3400747E-02 2.016670 at 20iterations 1.3532190E-03 0.2060242 at 30iterations 1.4168164E-04 2.3056030E-02 at 40iterations 1.3993316E-05 2.7351379E-03 at 50iterations finished qdiffx linear iterations at : 11:02:01 total time elapsed so far: 4.610000 # loops : 50 mean,max change (kT/e) : 1.3993316E-05 2.7351379E-03 energy calculations done at 4.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.810000 DelPhi exited at 11:02:03 4.815u 0.454s 0:07.57 69.4% 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 Wed Dec 28 2011 at 11:02:03 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 1.943621 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): -4.966000 34.23200 ymin,ymax (A): -3.439000 49.61500 zmin,zma (A): -23.77200 31.17700 x,y,z range (A): 39.19800 53.05400 54.94900 scale (grids/A): 1.943621 object centre (A): 14.63300 23.08800 3.702500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 291.8019 centred at (gu) : 91.28466 96.09265 90.04253 assigned negative charge : -288.4402 centred at (gu) : 91.61714 96.53033 89.81894 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 60587 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17189 grid for indexing accessible points = 1.400000 m= 22087 mr = 41773 m= 3205 mr = 16898 m= 143 mr = 2012 m= 3 mr = 43 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2296 time to turn everything in is 0.5900000 number of dielectric boundary points 25300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 14462 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) : 0.6478735 object centre at (A) : 14.63300 23.08800 3.702500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5062937E-02 1.4757991E-02 midg,1,midg; midg,igrid,midg 4.7395200E-02 -1.2390012E-02 1,midg,midg; igrid,midg,midg 8.8251736E-03 -4.0353313E-03 gauss-seidel spectral radius is 0.9986104 estimated iterations to convergence 213 setup time was (sec) 0.8700000 now iterating at: 11:02:04 rms-change max change #iterations 3.760249 167.3277 at 10iterations 1.746587 85.83707 at 20iterations 0.8143877 29.47068 at 30iterations 0.3782375 12.61914 at 40iterations 0.1759817 5.937686 at 50iterations 8.1620723E-02 2.935749 at 60iterations 3.8031321E-02 1.279938 at 70iterations 1.7670637E-02 0.6272278 at 80iterations 8.1975255E-03 0.2880210 at 90iterations 3.8157091E-03 0.1339550 at 100iterations 1.7844493E-03 5.9772491E-02 at 110iterations 8.2662626E-04 2.8644562E-02 at 120iterations finished qdiffx linear iterations at : 11:02:15 total time elapsed so far: 11.63000 # loops : 120 mean,max change (kT/e) : 8.2662626E-04 2.8644562E-02 energy calculations done at 11.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 11:02:18 11.816u 0.458s 0:14.50 84.5% 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 Wed Dec 28 2011 at 11:02:18 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 2.915431 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): -4.966000 34.23200 ymin,ymax (A): -3.439000 49.61500 zmin,zma (A): -23.77200 31.17700 x,y,z range (A): 39.19800 53.05400 54.94900 scale (grids/A): 2.915431 object centre (A): 14.63300 23.08800 3.702500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 291.8019 centred at (gu) : 91.92704 99.13890 90.06393 assigned negative charge : -288.4402 centred at (gu) : 92.42585 99.79547 89.72853 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 139889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17189 grid for indexing accessible points = 1.400000 m= 71495 mr = 100975 m= 25753 mr = 59413 m= 5598 mr = 21383 m= 661 mr = 4231 m= 40 mr = 424 m= 0 mr = 15 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 7670 time to turn everything in is 1.400000 number of dielectric boundary points 56995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 14656 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) : 1.943621 object centre at (A) : 14.63300 23.08800 3.702500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.001979 1.6919522E-03 midg,1,midg; midg,igrid,midg 0.4971220 -0.1709906 1,midg,midg; igrid,midg,midg 6.1505452E-02 -2.0226061E-02 gauss-seidel spectral radius is 0.9992374 estimated iterations to convergence 286 setup time was (sec) 1.730000 now iterating at: 11:02:20 rms-change max change #iterations 8.795329 429.0273 at 10iterations 5.045111 138.8370 at 20iterations 2.875628 64.83676 at 30iterations 1.640797 36.73031 at 40iterations 0.9356183 25.10721 at 50iterations 0.5326654 10.57025 at 60iterations 0.3025036 6.182826 at 70iterations 0.1716660 3.511461 at 80iterations 9.8199926E-02 2.296295 at 90iterations 5.5723824E-02 1.070106 at 100iterations 3.1697448E-02 0.6785278 at 110iterations 1.7940069E-02 0.3423433 at 120iterations 1.0220857E-02 0.1911697 at 130iterations 5.8000609E-03 0.1104932 at 140iterations 3.3059351E-03 7.6946259E-02 at 150iterations 1.8792312E-03 4.0542603E-02 at 160iterations 1.0675263E-03 2.3170471E-02 at 170iterations 6.0833164E-04 1.1815071E-02 at 180iterations finished qdiffx linear iterations at : 11:02:38 total time elapsed so far: 19.31000 # loops : 180 mean,max change (kT/e) : 6.0833164E-04 1.1815071E-02 energy calculations done at 19.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.50000 DelPhi exited at 11:02:39 19.505u 0.362s 0:21.47 92.5% 0+0k 0+0io 0pf+0w