Tue Oct 11 08:16:04 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 Tue Oct 11 2011 at 08:16:04 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: FMN 398 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6820708 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): 4.116000 56.31000 ymin,ymax (A): -3.785000 42.35100 zmin,zma (A): -29.84800 17.34500 x,y,z range (A): 52.19400 46.13600 47.19300 scale (grids/A): 0.6820708 object centre (A): 30.21300 19.28300 -6.251500 number of atom coordinates read : 2760 total number of charged atoms : 2625 net assigned charge : 5.000019 assigned positive charge : 426.0113 centred at (gu) : 90.98647 89.98972 89.35945 assigned negative charge : -421.0124 centred at (gu) : 90.73557 89.95646 89.31760 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8682 nv = 96 ne = 84 npr = 57048 no. pairs analyzed = 57048 no. exposed pairs = 3395 no. arc points = 22946 no. surface atoms = 1134 nbur = 1626 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 516 mr = 5001 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.2200000 number of dielectric boundary points 4116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2181 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9990 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9567161E-09 3.2855574E-08 midg,1,midg; midg,igrid,midg 9.4954027E-09 3.4071874E-08 1,midg,midg; igrid,midg,midg -5.9908437E-08 1.3773376E-07 gauss-seidel spectral radius is 0.9888678 estimated iterations to convergence 77 setup time was (sec) 0.4000000 now iterating at: 08:16:05 rms-change max change #iterations 0.2047011 33.14227 at 10iterations 2.4328193E-02 3.562672 at 20iterations 3.8876240E-03 0.6644287 at 30iterations 1.1902162E-03 0.2379150 at 40iterations 4.7406883E-04 9.6160889E-02 at 50iterations finished qdiffx linear iterations at : 08:16:08 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 4.7406883E-04 9.6160889E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 08:16:08 3.425u 0.187s 0:03.89 92.5% 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 08:16:08 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: FMN 398 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.046212 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): 4.116000 56.31000 ymin,ymax (A): -3.785000 42.35100 zmin,zma (A): -29.84800 17.34500 x,y,z range (A): 52.19400 46.13600 47.19300 scale (grids/A): 2.046212 object centre (A): 30.21300 19.28300 -6.251500 number of atom coordinates read : 2760 total number of charged atoms : 2625 net assigned charge : 5.000019 assigned positive charge : 426.0113 centred at (gu) : 92.95918 89.96866 88.07746 assigned negative charge : -421.0124 centred at (gu) : 92.20666 89.86900 87.95270 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 92756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22946 grid for indexing accessible points = 1.400000 m= 35817 mr = 65901 m= 6482 mr = 27357 m= 505 mr = 4365 m= 7 mr = 246 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1139 time to turn everything in is 0.4500000 number of dielectric boundary points 37698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 20820 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) : 0.6820708 object centre at (A) : 30.21300 19.28300 -6.251500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1963337E-02 -2.1349059E-02 midg,1,midg; midg,igrid,midg 3.1928960E-02 2.6919756E-02 1,midg,midg; igrid,midg,midg -2.0368911E-02 9.1742590E-02 gauss-seidel spectral radius is 0.9988232 estimated iterations to convergence 231 setup time was (sec) 0.6700000 now iterating at: 08:16:09 rms-change max change #iterations 5.132646 259.8560 at 10iterations 2.528643 80.15676 at 20iterations 1.247787 36.78624 at 30iterations 0.6168035 21.52925 at 40iterations 0.3064995 8.159729 at 50iterations 0.1512484 4.072752 at 60iterations 7.5159989E-02 2.066076 at 70iterations 3.7480660E-02 1.112700 at 80iterations 1.8857421E-02 0.5191536 at 90iterations 9.6593825E-03 0.3055940 at 100iterations 5.1528914E-03 0.1685028 at 110iterations 2.8960078E-03 9.9903107E-02 at 120iterations finished qdiffx linear iterations at : 08:16:16 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 2.8960078E-03 9.9903107E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 08:16:17 7.882u 0.209s 0:08.55 94.5% 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 08:16:17 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: FMN 398 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.069319 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): 4.116000 56.31000 ymin,ymax (A): -3.785000 42.35100 zmin,zma (A): -29.84800 17.34500 x,y,z range (A): 52.19400 46.13600 47.19300 scale (grids/A): 3.069319 object centre (A): 30.21300 19.28300 -6.251500 number of atom coordinates read : 2760 total number of charged atoms : 2625 net assigned charge : 5.000019 assigned positive charge : 426.0113 centred at (gu) : 94.43855 89.95283 87.11588 assigned negative charge : -421.0124 centred at (gu) : 93.30975 89.80338 86.92895 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 214206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22946 grid for indexing accessible points = 1.400000 m= 113129 mr = 159111 m= 44807 mr = 94211 m= 12083 mr = 37227 m= 2151 mr = 9367 m= 211 mr = 1598 m= 6 mr = 113 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7099999 no. cavity mid-points inaccessible to solvent = 3519 time to turn everything in is 1.200000 number of dielectric boundary points 84967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 21000 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) : 2.046212 object centre at (A) : 30.21300 19.28300 -6.251500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3784007 -0.2670933 midg,1,midg; midg,igrid,midg 0.3823289 0.1759766 1,midg,midg; igrid,midg,midg -0.2933537 0.5278951 gauss-seidel spectral radius is 0.9993048 estimated iterations to convergence 299 setup time was (sec) 1.440000 now iterating at: 08:16:18 rms-change max change #iterations 11.58867 412.6324 at 10iterations 6.842032 123.1503 at 20iterations 4.038318 71.15096 at 30iterations 2.379830 42.72173 at 40iterations 1.397498 23.37534 at 50iterations 0.8228763 13.14256 at 60iterations 0.4834022 7.967552 at 70iterations 0.2841624 4.908337 at 80iterations 0.1664769 2.803963 at 90iterations 9.7679786E-02 1.756687 at 100iterations 5.7371590E-02 0.9545803 at 110iterations 3.3879854E-02 0.5372620 at 120iterations 2.0115033E-02 0.3746529 at 130iterations 1.2100271E-02 0.2032127 at 140iterations 7.4716657E-03 0.1408043 at 150iterations 4.8282770E-03 0.1007061 at 160iterations 3.3278316E-03 7.6026917E-02 at 170iterations 2.4476303E-03 5.9158325E-02 at 180iterations finished qdiffx linear iterations at : 08:16:30 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 2.4476303E-03 5.9158325E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 08:16:30 13.137u 0.213s 0:13.74 97.0% 0+0k 0+0io 0pf+0w