Tue Oct 11 08:34:47 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 08:34:47 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7076409 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): 0.2689999 46.95500 ymin,ymax (A): 0.6079999 41.14400 zmin,zma (A): -3.280000 47.02800 x,y,z range (A): 46.68600 40.53600 50.30800 scale (grids/A): 0.7076409 object centre (A): 23.61200 20.87600 21.87400 number of atom coordinates read : 2071 total number of charged atoms : 1965 net assigned charge : 5.550011 assigned positive charge : 321.3842 centred at (gu) : 90.94279 90.26161 90.71062 assigned negative charge : -315.8341 centred at (gu) : 91.09010 90.22369 90.77643 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7003 nv = 96 ne = 84 npr = 41502 no. pairs analyzed = 41502 no. exposed pairs = 2510 no. arc points = 17014 no. surface atoms = 854 nbur = 1217 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4049 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1626 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7820 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0571787E-08 1.6613091E-08 midg,1,midg; midg,igrid,midg 2.7620962E-08 7.0474620E-08 1,midg,midg; igrid,midg,midg 1.0074505E-07 -3.3286572E-08 gauss-seidel spectral radius is 0.9895877 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 08:34:48 rms-change max change #iterations 0.1995037 28.22695 at 10iterations 2.5506845E-02 4.013703 at 20iterations 3.4145277E-03 0.4991989 at 30iterations 5.5741589E-04 9.1678619E-02 at 40iterations 1.3744341E-04 2.1282196E-02 at 50iterations finished qdiffx linear iterations at : 08:34:50 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.3744341E-04 2.1282196E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 08:34:51 3.337u 0.169s 0:04.09 85.3% 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 08:34:51 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.122923 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): 0.2689999 46.95500 ymin,ymax (A): 0.6079999 41.14400 zmin,zma (A): -3.280000 47.02800 x,y,z range (A): 46.68600 40.53600 50.30800 scale (grids/A): 2.122923 object centre (A): 23.61200 20.87600 21.87400 number of atom coordinates read : 2071 total number of charged atoms : 1965 net assigned charge : 5.550011 assigned positive charge : 321.3842 centred at (gu) : 92.82844 90.78489 92.13210 assigned negative charge : -315.8341 centred at (gu) : 93.27037 90.67116 92.32941 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74638 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17014 grid for indexing accessible points = 1.400000 m= 29709 mr = 53236 m= 5632 mr = 22594 m= 458 mr = 3727 m= 9 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 30654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 15591 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) : 0.7076409 object centre at (A) : 23.61200 20.87600 21.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5884795E-02 6.5513238E-02 midg,1,midg; midg,igrid,midg -4.3903613E-03 3.1628709E-02 1,midg,midg; igrid,midg,midg 2.7170194E-02 6.6303420E-03 gauss-seidel spectral radius is 0.9988278 estimated iterations to convergence 231 setup time was (sec) 0.5900000 now iterating at: 08:34:52 rms-change max change #iterations 4.690092 182.2940 at 10iterations 2.319427 74.01045 at 20iterations 1.147740 35.95047 at 30iterations 0.5709676 17.30541 at 40iterations 0.2842411 8.663704 at 50iterations 0.1407369 4.323212 at 60iterations 6.9840617E-02 2.237896 at 70iterations 3.4703266E-02 1.013522 at 80iterations 1.7392660E-02 0.5015116 at 90iterations 8.6967004E-03 0.2952824 at 100iterations 4.3690698E-03 0.1418028 at 110iterations 2.2367779E-03 7.4848175E-02 at 120iterations finished qdiffx linear iterations at : 08:34:59 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 2.2367779E-03 7.4848175E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 08:35:00 7.764u 0.197s 0:08.49 93.6% 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 Tue Oct 11 2011 at 08:35:00 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.184384 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): 0.2689999 46.95500 ymin,ymax (A): 0.6079999 41.14400 zmin,zma (A): -3.280000 47.02800 x,y,z range (A): 46.68600 40.53600 50.30800 scale (grids/A): 3.184384 object centre (A): 23.61200 20.87600 21.87400 number of atom coordinates read : 2071 total number of charged atoms : 1965 net assigned charge : 5.550011 assigned positive charge : 321.3842 centred at (gu) : 94.24273 91.17731 93.19808 assigned negative charge : -315.8341 centred at (gu) : 94.90559 91.00690 93.49413 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 172036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17014 grid for indexing accessible points = 1.400000 m= 93504 mr = 128289 m= 37296 mr = 77989 m= 10593 mr = 30630 m= 1968 mr = 8175 m= 213 mr = 1404 m= 3 mr = 128 m= 0 mr = 2 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.140000 number of dielectric boundary points 68996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 15720 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) : 2.122923 object centre at (A) : 23.61200 20.87600 21.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3465163 0.6875261 midg,1,midg; midg,igrid,midg -8.5260957E-02 0.2443987 1,midg,midg; igrid,midg,midg 0.2308235 0.2829745 gauss-seidel spectral radius is 0.9992937 estimated iterations to convergence 297 setup time was (sec) 1.370000 now iterating at: 08:35:01 rms-change max change #iterations 10.42992 372.7421 at 10iterations 6.168146 129.4037 at 20iterations 3.626552 70.44473 at 30iterations 2.135576 38.73854 at 40iterations 1.251638 23.22577 at 50iterations 0.7354644 15.65696 at 60iterations 0.4301845 7.795601 at 70iterations 0.2522798 4.623633 at 80iterations 0.1473943 2.605909 at 90iterations 8.6361594E-02 1.573298 at 100iterations 5.0551936E-02 0.8971252 at 110iterations 2.9685387E-02 0.5622940 at 120iterations 1.7537693E-02 0.3340244 at 130iterations 1.0484256E-02 0.1798382 at 140iterations 6.3824458E-03 0.1127033 at 150iterations 3.9985524E-03 8.2286835E-02 at 160iterations 2.6259606E-03 4.6096802E-02 at 170iterations 1.8233126E-03 3.2341003E-02 at 180iterations finished qdiffx linear iterations at : 08:35:13 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 1.8233126E-03 3.2341003E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 08:35:13 12.705u 0.207s 0:13.35 96.6% 0+0k 0+0io 0pf+0w