Sat Oct 8 17:47:58 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 Sat Oct 8 2011 at 17:47:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3508 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5245090 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): -0.9960000 44.14800 ymin,ymax (A): -30.76300 25.73900 zmin,zma (A): 1.371000 69.24400 x,y,z range (A): 45.14400 56.50200 67.87300 scale (grids/A): 0.5245090 object centre (A): 21.57600 -2.512000 35.30750 number of atom coordinates read : 3508 total number of charged atoms : 3361 net assigned charge : -5.771982 assigned positive charge : 531.5441 centred at (gu) : 90.46233 92.00623 90.60413 assigned negative charge : -537.3177 centred at (gu) : 90.42235 91.96635 90.59227 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6067 nv = 96 ne = 84 npr = 71704 no. pairs analyzed = 71704 no. exposed pairs = 4207 no. arc points = 28897 no. surface atoms = 1430 nbur = 2078 mkacc time = 0.1600000 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 = 1.624000 m= 217 mr = 3260 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2873 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8126 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6699470E-10 -1.3019044E-10 midg,1,midg; midg,igrid,midg -1.7612155E-10 -2.0813008E-11 1,midg,midg; igrid,midg,midg -2.5997079E-10 -1.6516427E-11 gauss-seidel spectral radius is 0.9813090 estimated iterations to convergence 60 setup time was (sec) 0.6300000 now iterating at: 17:47:59 rms-change max change #iterations 6.4813577E-02 11.77548 at 10iterations 4.0366664E-03 0.6010342 at 20iterations 3.3874970E-04 6.7854881E-02 at 30iterations 6.2749838E-05 1.4535904E-02 at 40iterations 1.4952529E-05 3.5114288E-03 at 50iterations finished qdiffx linear iterations at : 17:48:03 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.4952529E-05 3.5114288E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 17:48:03 4.215u 0.221s 0:04.71 94.0% 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 Sat Oct 8 2011 at 17:48:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3508 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.573527 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): -0.9960000 44.14800 ymin,ymax (A): -30.76300 25.73900 zmin,zma (A): 1.371000 69.24400 x,y,z range (A): 45.14400 56.50200 67.87300 scale (grids/A): 1.573527 object centre (A): 21.57600 -2.512000 35.30750 number of atom coordinates read : 3508 total number of charged atoms : 3361 net assigned charge : -5.771982 assigned positive charge : 531.5441 centred at (gu) : 91.38618 96.01724 91.81124 assigned negative charge : -537.3177 centred at (gu) : 91.26662 95.89867 91.77633 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28897 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20417 mr = 48234 m= 1794 mr = 14014 m= 32 mr = 828 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 224 time to turn everything in is 0.5200000 number of dielectric boundary points 28147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 438 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 25521 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) : 0.5245090 object centre at (A) : 21.57600 -2.512000 35.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5493241E-03 1.2293024E-02 midg,1,midg; midg,igrid,midg -7.6192538E-03 -1.1987316E-02 1,midg,midg; igrid,midg,midg -4.1420385E-03 4.6487647E-04 gauss-seidel spectral radius is 0.9980794 estimated iterations to convergence 181 setup time was (sec) 0.8600000 now iterating at: 17:48:04 rms-change max change #iterations 3.348992 141.3455 at 10iterations 1.359918 50.02521 at 20iterations 0.5524979 19.74536 at 30iterations 0.2259748 8.808105 at 40iterations 9.2139341E-02 3.142731 at 50iterations 3.7491467E-02 1.478733 at 60iterations 1.5281440E-02 0.5568829 at 70iterations 6.2573543E-03 0.2546482 at 80iterations 2.5762215E-03 8.7574959E-02 at 90iterations 1.0738000E-03 3.9089203E-02 at 100iterations 4.6345979E-04 2.0141125E-02 at 110iterations 2.1097004E-04 8.7661743E-03 at 120iterations finished qdiffx linear iterations at : 17:48:13 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 2.1097004E-04 8.7661743E-03 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.470000 DelPhi exited at 17:48:13 9.470u 0.238s 0:09.98 97.1% 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 Sat Oct 8 2011 at 17:48:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3508 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.360291 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): -0.9960000 44.14800 ymin,ymax (A): -30.76300 25.73900 zmin,zma (A): 1.371000 69.24400 x,y,z range (A): 45.14400 56.50200 67.87300 scale (grids/A): 2.360291 object centre (A): 21.57600 -2.512000 35.30750 number of atom coordinates read : 3508 total number of charged atoms : 3361 net assigned charge : -5.771982 assigned positive charge : 531.5441 centred at (gu) : 92.07901 99.02565 92.71683 assigned negative charge : -537.3177 centred at (gu) : 91.89995 98.84772 92.66442 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 160688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28897 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73186 mr = 117893 m= 18902 mr = 58333 m= 2506 mr = 14067 m= 110 mr = 1562 m= 3 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 713 time to turn everything in is 1.250000 number of dielectric boundary points 63511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 26833 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) : 1.573527 object centre at (A) : 21.57600 -2.512000 35.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2020456 0.1178104 midg,1,midg; midg,igrid,midg -0.1066463 -0.1590180 1,midg,midg; igrid,midg,midg -7.8458957E-02 2.7984733E-02 gauss-seidel spectral radius is 0.9991089 estimated iterations to convergence 265 setup time was (sec) 1.600000 now iterating at: 17:48:15 rms-change max change #iterations 8.851312 261.6372 at 10iterations 4.899811 125.8180 at 20iterations 2.699374 60.25125 at 30iterations 1.479962 28.44773 at 40iterations 0.8094909 16.39289 at 50iterations 0.4424186 8.915886 at 60iterations 0.2409882 4.988036 at 70iterations 0.1314289 3.081378 at 80iterations 7.1709260E-02 1.676429 at 90iterations 3.9014921E-02 0.7980661 at 100iterations 2.1183625E-02 0.4149704 at 110iterations 1.1552788E-02 0.2356987 at 120iterations 6.3066673E-03 0.1202660 at 130iterations 3.4357107E-03 6.3657761E-02 at 140iterations 1.8784616E-03 3.8108587E-02 at 150iterations 1.0287119E-03 2.1244526E-02 at 160iterations 5.6760549E-04 1.1315346E-02 at 170iterations 3.1689653E-04 7.9612732E-03 at 180iterations finished qdiffx linear iterations at : 17:48:28 total time elapsed so far: 14.86000 # loops : 180 mean,max change (kT/e) : 3.1689653E-04 7.9612732E-03 energy calculations done at 14.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.05000 DelPhi exited at 17:48:29 15.050u 0.255s 0:15.58 98.2% 0+0k 0+0io 0pf+0w