Tue Oct 11 06:53:07 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 06:53:07 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3162 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5544913 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): -19.96900 44.23400 ymin,ymax (A): 19.45200 77.34900 zmin,zma (A): -69.40701 -21.49500 x,y,z range (A): 64.20300 57.89700 47.91200 scale (grids/A): 0.5544913 object centre (A): 12.13250 48.40050 -45.45100 number of atom coordinates read : 3162 total number of charged atoms : 3017 net assigned charge : -3.099988 assigned positive charge : 465.7672 centred at (gu) : 89.87258 90.09398 89.98313 assigned negative charge : -468.8679 centred at (gu) : 89.94213 90.29477 90.01941 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6254 nv = 96 ne = 84 npr = 65618 no. pairs analyzed = 65618 no. exposed pairs = 4051 no. arc points = 28450 no. surface atoms = 1367 nbur = 1795 mkacc time = 0.1400000 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= 306 mr = 3238 m= 0 mr = 23 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3600000 number of dielectric boundary points 3299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2852 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8208 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2263182E-11 -6.1201411E-10 midg,1,midg; midg,igrid,midg 1.5776696E-09 -2.2935316E-09 1,midg,midg; igrid,midg,midg 4.1020828E-10 -9.0926555E-10 gauss-seidel spectral radius is 0.9832419 estimated iterations to convergence 64 setup time was (sec) 0.5900000 now iterating at: 06:53:08 rms-change max change #iterations 8.1581958E-02 14.69728 at 10iterations 5.6807599E-03 0.8255467 at 20iterations 4.0370889E-04 6.1891556E-02 at 30iterations 3.4218941E-05 5.7201385E-03 at 40iterations 5.1914644E-06 1.0757446E-03 at 50iterations finished qdiffx linear iterations at : 06:53:11 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 5.1914644E-06 1.0757446E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 06:53:11 3.472u 0.208s 0:04.11 89.2% 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 06:53:11 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3162 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 1.663474 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): -19.96900 44.23400 ymin,ymax (A): 19.45200 77.34900 zmin,zma (A): -69.40701 -21.49500 x,y,z range (A): 64.20300 57.89700 47.91200 scale (grids/A): 1.663474 object centre (A): 12.13250 48.40050 -45.45100 number of atom coordinates read : 3162 total number of charged atoms : 3017 net assigned charge : -3.099988 assigned positive charge : 465.7672 centred at (gu) : 89.61736 90.28125 89.94880 assigned negative charge : -468.8679 centred at (gu) : 89.82585 90.88377 90.05776 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68226 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23021 mr = 45623 m= 3061 mr = 16424 m= 96 mr = 1771 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 493 time to turn everything in is 0.5200000 number of dielectric boundary points 30563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 279 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 23248 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) : 0.5544913 object centre at (A) : 12.13250 48.40050 -45.45100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7189448E-03 1.0568891E-02 midg,1,midg; midg,igrid,midg 9.7395043E-04 -1.2093447E-02 1,midg,midg; igrid,midg,midg 6.8733525E-03 -3.5761334E-02 gauss-seidel spectral radius is 0.9982758 estimated iterations to convergence 191 setup time was (sec) 0.8200000 now iterating at: 06:53:12 rms-change max change #iterations 3.521975 199.6403 at 10iterations 1.501224 53.55920 at 20iterations 0.6378248 22.54650 at 30iterations 0.2715781 8.895794 at 40iterations 0.1158458 3.916269 at 50iterations 4.9249183E-02 1.700202 at 60iterations 2.1059256E-02 0.7131615 at 70iterations 8.9604305E-03 0.3373313 at 80iterations 3.8275323E-03 0.1350999 at 90iterations 1.6392344E-03 5.4565430E-02 at 100iterations 6.9913402E-04 2.3139000E-02 at 110iterations 2.9944256E-04 1.0375977E-02 at 120iterations finished qdiffx linear iterations at : 06:53:19 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 2.9944256E-04 1.0375977E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 06:53:20 7.720u 0.257s 0:08.32 95.7% 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 06:53:20 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3162 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.495211 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): -19.96900 44.23400 ymin,ymax (A): 19.45200 77.34900 zmin,zma (A): -69.40701 -21.49500 x,y,z range (A): 64.20300 57.89700 47.91200 scale (grids/A): 2.495211 object centre (A): 12.13250 48.40050 -45.45100 number of atom coordinates read : 3162 total number of charged atoms : 3017 net assigned charge : -3.099988 assigned positive charge : 465.7672 centred at (gu) : 89.42582 90.42162 89.92287 assigned negative charge : -468.8679 centred at (gu) : 89.73840 91.32545 90.08669 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 157826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 75809 mr = 111574 m= 25875 mr = 60300 m= 5203 mr = 20440 m= 474 mr = 3751 m= 15 mr = 261 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 1762 time to turn everything in is 1.200000 number of dielectric boundary points 68874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 24112 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) : 1.663474 object centre at (A) : 12.13250 48.40050 -45.45100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1226437 0.2136577 midg,1,midg; midg,igrid,midg -2.7486963E-02 -0.1153275 1,midg,midg; igrid,midg,midg 5.4575000E-02 -0.7970340 gauss-seidel spectral radius is 0.9991705 estimated iterations to convergence 274 setup time was (sec) 1.530000 now iterating at: 06:53:21 rms-change max change #iterations 9.083291 356.3477 at 10iterations 5.136855 133.4885 at 20iterations 2.892723 64.15735 at 30iterations 1.626199 36.95409 at 40iterations 0.9086497 18.73786 at 50iterations 0.5072784 10.40583 at 60iterations 0.2834307 6.101385 at 70iterations 0.1581143 3.037800 at 80iterations 8.7999530E-02 1.833603 at 90iterations 4.8837647E-02 0.9694495 at 100iterations 2.7196627E-02 0.6153107 at 110iterations 1.5100271E-02 0.3067017 at 120iterations 8.3989277E-03 0.1654510 at 130iterations 4.6633827E-03 9.5115483E-02 at 140iterations 2.5996014E-03 5.5992126E-02 at 150iterations 1.4467133E-03 2.9127121E-02 at 160iterations 8.0647517E-04 1.4930725E-02 at 170iterations 4.5382328E-04 8.5639954E-03 at 180iterations finished qdiffx linear iterations at : 06:53:32 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 4.5382328E-04 8.5639954E-03 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 06:53:33 12.479u 0.253s 0:13.04 97.5% 0+0k 0+0io 0pf+0w