Mon Oct 10 14:19:21 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 Mon Oct 10 2011 at 14:19:21 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3114 !!! WARNING: TPO 301 has a net charge of -0.2260 !!! WARNING: SEP 320 has a net charge of -0.2020 !!! WARNING: TPO 1 has a net charge of -1.2740 !!! WARNING: TPO 2 has a net charge of -1.2740 !!! WARNING: SEP 3 has a net charge of -1.2980 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: 0.6011584 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): 7.679000 62.95900 ymin,ymax (A): 22.76800 81.98700 zmin,zma (A): 5.895000 61.13200 x,y,z range (A): 55.28000 59.21900 55.23700 scale (grids/A): 0.6011584 object centre (A): 35.31900 52.37750 33.51350 number of atom coordinates read : 3114 total number of charged atoms : 2964 net assigned charge : -12.77398 assigned positive charge : 455.0293 centred at (gu) : 89.27450 89.33241 89.03395 assigned negative charge : -467.8039 centred at (gu) : 89.38300 89.30775 88.81011 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7848 nv = 96 ne = 84 npr = 60873 no. pairs analyzed = 60873 no. exposed pairs = 4327 no. arc points = 31405 no. surface atoms = 1436 nbur = 1678 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 3967 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3062 ## 291 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9545 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9985134E-08 3.4328878E-09 midg,1,midg; midg,igrid,midg -7.7731332E-09 -3.8632040E-09 1,midg,midg; igrid,midg,midg -7.7523055E-10 -8.9928225E-09 gauss-seidel spectral radius is 0.9857425 estimated iterations to convergence 69 setup time was (sec) 0.4000000 now iterating at: 14:19:22 rms-change max change #iterations 0.1211802 21.74694 at 10iterations 1.0663997E-02 1.389080 at 20iterations 1.3921717E-03 0.2526245 at 30iterations 4.2559419E-04 9.2046738E-02 at 40iterations 1.6527699E-04 3.5797119E-02 at 50iterations finished qdiffx linear iterations at : 14:19:24 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.6527699E-04 3.5797119E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 14:19:25 3.359u 0.188s 0:03.88 90.9% 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 Mon Oct 10 2011 at 14:19:25 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3114 !!! WARNING: TPO 301 has a net charge of -0.2260 !!! WARNING: SEP 320 has a net charge of -0.2020 !!! WARNING: TPO 1 has a net charge of -1.2740 !!! WARNING: TPO 2 has a net charge of -1.2740 !!! WARNING: SEP 3 has a net charge of -1.2980 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: 1.803475 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): 7.679000 62.95900 ymin,ymax (A): 22.76800 81.98700 zmin,zma (A): 5.895000 61.13200 x,y,z range (A): 55.28000 59.21900 55.23700 scale (grids/A): 1.803475 object centre (A): 35.31900 52.37750 33.51350 number of atom coordinates read : 3114 total number of charged atoms : 2964 net assigned charge : -12.77398 assigned positive charge : 455.0293 centred at (gu) : 87.82320 87.99651 87.10098 assigned negative charge : -467.8039 centred at (gu) : 88.14857 87.92307 86.43000 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31405 grid for indexing accessible points = 1.400000 m= 28927 mr = 55861 m= 3933 mr = 20292 m= 210 mr = 2198 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 323 time to turn everything in is 0.4100000 number of dielectric boundary points 39491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 231 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 23178 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) : 0.6011584 object centre at (A) : 35.31900 52.37750 33.51350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8473205E-02 1.1170418E-03 midg,1,midg; midg,igrid,midg -1.0878819E-02 -9.0497648E-03 1,midg,midg; igrid,midg,midg -1.3339444E-02 -3.9860364E-02 gauss-seidel spectral radius is 0.9985590 estimated iterations to convergence 209 setup time was (sec) 0.6300000 now iterating at: 14:19:26 rms-change max change #iterations 4.258011 202.8929 at 10iterations 1.944569 64.15384 at 20iterations 0.8825431 32.58446 at 30iterations 0.4038002 12.01955 at 40iterations 0.1848664 6.249744 at 50iterations 8.4723055E-02 2.632613 at 60iterations 3.8692091E-02 1.154604 at 70iterations 1.7869469E-02 0.5586929 at 80iterations 8.2978895E-03 0.2709198 at 90iterations 3.9228727E-03 0.1255493 at 100iterations 1.9340829E-03 6.6093445E-02 at 110iterations 1.0299704E-03 4.0748596E-02 at 120iterations finished qdiffx linear iterations at : 14:19:33 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 1.0299704E-03 4.0748596E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 14:19:34 7.978u 0.222s 0:08.67 94.4% 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 Mon Oct 10 2011 at 14:19:34 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3114 !!! WARNING: TPO 301 has a net charge of -0.2260 !!! WARNING: SEP 320 has a net charge of -0.2020 !!! WARNING: TPO 1 has a net charge of -1.2740 !!! WARNING: TPO 2 has a net charge of -1.2740 !!! WARNING: SEP 3 has a net charge of -1.2980 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: 2.705213 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): 7.679000 62.95900 ymin,ymax (A): 22.76800 81.98700 zmin,zma (A): 5.895000 61.13200 x,y,z range (A): 55.28000 59.21900 55.23700 scale (grids/A): 2.705213 object centre (A): 35.31900 52.37750 33.51350 number of atom coordinates read : 3114 total number of charged atoms : 2964 net assigned charge : -12.77398 assigned positive charge : 455.0293 centred at (gu) : 86.73458 86.99458 85.65141 assigned negative charge : -467.8039 centred at (gu) : 87.22264 86.88451 84.64487 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 195927 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31405 grid for indexing accessible points = 1.400000 m= 94693 mr = 136431 m= 32108 mr = 74996 m= 6696 mr = 24744 m= 812 mr = 4690 m= 43 mr = 461 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 1026 time to turn everything in is 1.040000 number of dielectric boundary points 88944 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 23697 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) : 1.803475 object centre at (A) : 35.31900 52.37750 33.51350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4233119 5.0681245E-02 midg,1,midg; midg,igrid,midg -7.7837631E-02 -0.1912259 1,midg,midg; igrid,midg,midg -0.2275057 -0.3586803 gauss-seidel spectral radius is 0.9992603 estimated iterations to convergence 290 setup time was (sec) 1.270000 now iterating at: 14:19:35 rms-change max change #iterations 10.44203 308.7458 at 10iterations 6.180366 135.5048 at 20iterations 3.619931 88.23775 at 30iterations 2.108220 48.07505 at 40iterations 1.225737 24.29041 at 50iterations 0.7083846 12.56510 at 60iterations 0.4092564 8.221161 at 70iterations 0.2362420 4.624825 at 80iterations 0.1361849 2.488794 at 90iterations 7.8656986E-02 1.454313 at 100iterations 4.5361366E-02 0.8817387 at 110iterations 2.5998155E-02 0.4532108 at 120iterations 1.4992331E-02 0.2756424 at 130iterations 8.6901337E-03 0.1643906 at 140iterations 5.0408747E-03 0.1007805 at 150iterations 2.9460064E-03 5.9301376E-02 at 160iterations 1.7531984E-03 3.6172867E-02 at 170iterations 1.0772436E-03 2.2615910E-02 at 180iterations finished qdiffx linear iterations at : 14:19:47 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 1.0772436E-03 2.2615910E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 14:19:47 12.972u 0.228s 0:13.54 97.4% 0+0k 0+0io 0pf+0w