Sat Oct 8 11:48:49 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 11:48:49 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 = 4430 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: 0.5629349 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): -27.66600 35.27100 ymin,ymax (A): 35.24400 98.48400 zmin,zma (A): 31.24300 91.06000 x,y,z range (A): 62.93700 63.24000 59.81699 scale (grids/A): 0.5629349 object centre (A): 3.802500 66.86400 61.15150 number of atom coordinates read : 4430 total number of charged atoms : 4269 net assigned charge : -7.499953 assigned positive charge : 667.7820 centred at (gu) : 90.49892 88.19862 88.55608 assigned negative charge : -675.2853 centred at (gu) : 90.33894 88.24293 88.69458 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8927 nv = 96 ne = 84 npr = 92936 no. pairs analyzed = 92936 no. exposed pairs = 5020 no. arc points = 33957 no. surface atoms = 1696 nbur = 2734 mkacc time = 0.2400000 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 = 1.540000 m= 395 mr = 5137 m= 0 mr = 33 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.4700000 number of dielectric boundary points 4152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3539 ## 426 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2696762E-09 -2.5239273E-09 midg,1,midg; midg,igrid,midg -1.8300907E-10 -1.1630941E-09 1,midg,midg; igrid,midg,midg -3.5306569E-09 2.2196052E-09 gauss-seidel spectral radius is 0.9838216 estimated iterations to convergence 65 setup time was (sec) 0.7500000 now iterating at: 11:48:50 rms-change max change #iterations 0.1055782 14.15211 at 10iterations 8.2616741E-03 1.076622 at 20iterations 1.0296893E-03 0.1616287 at 30iterations 2.6077469E-04 4.1244507E-02 at 40iterations 8.4054722E-05 1.0852814E-02 at 50iterations finished qdiffx linear iterations at : 11:48:54 total time elapsed so far: 4.780000 # loops : 50 mean,max change (kT/e) : 8.4054722E-05 1.0852814E-02 energy calculations done at 4.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.960000 DelPhi exited at 11:48:55 4.960u 0.420s 0:05.64 95.3% 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 Sat Oct 8 2011 at 11:48:55 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 = 4430 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.688805 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): -27.66600 35.27100 ymin,ymax (A): 35.24400 98.48400 zmin,zma (A): 31.24300 91.06000 x,y,z range (A): 62.93700 63.24000 59.81699 scale (grids/A): 1.688805 object centre (A): 3.802500 66.86400 61.15150 number of atom coordinates read : 4430 total number of charged atoms : 4269 net assigned charge : -7.499953 assigned positive charge : 667.7820 centred at (gu) : 91.49532 84.59424 85.66698 assigned negative charge : -675.2853 centred at (gu) : 91.01635 84.72823 86.08315 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 100157 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33957 grid for indexing accessible points = 1.400000 m= 33529 mr = 72509 m= 3959 mr = 24503 m= 118 mr = 2297 m= 0 mr = 24 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 6236 time to turn everything in is 0.8300000 number of dielectric boundary points 38430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 348 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 32961 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) : 0.5629349 object centre at (A) : 3.802500 66.86400 61.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6398310E-02 -2.4684638E-02 midg,1,midg; midg,igrid,midg 1.5368441E-02 -7.0528663E-03 1,midg,midg; igrid,midg,midg -2.6752258E-02 2.7233584E-02 gauss-seidel spectral radius is 0.9984290 estimated iterations to convergence 200 setup time was (sec) 1.150000 now iterating at: 11:48:56 rms-change max change #iterations 4.524923 158.6497 at 10iterations 2.002291 71.42836 at 20iterations 0.8905650 25.17436 at 30iterations 0.3945345 12.10045 at 40iterations 0.1752703 5.840160 at 50iterations 7.7806547E-02 2.292748 at 60iterations 3.4606092E-02 1.008514 at 70iterations 1.5470569E-02 0.4449005 at 80iterations 6.9218660E-03 0.2265859 at 90iterations 3.1179043E-03 0.1050072 at 100iterations 1.4266982E-03 4.3186188E-02 at 110iterations 6.7083543E-04 1.9147635E-02 at 120iterations finished qdiffx linear iterations at : 11:49:07 total time elapsed so far: 11.72000 # loops : 120 mean,max change (kT/e) : 6.7083543E-04 1.9147635E-02 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.95000 DelPhi exited at 11:49:07 11.951u 0.471s 0:12.69 97.8% 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 11:49:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4430 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.533207 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): -27.66600 35.27100 ymin,ymax (A): 35.24400 98.48400 zmin,zma (A): 31.24300 91.06000 x,y,z range (A): 62.93700 63.24000 59.81699 scale (grids/A): 2.533207 object centre (A): 3.802500 66.86400 61.15150 number of atom coordinates read : 4430 total number of charged atoms : 4269 net assigned charge : -7.499953 assigned positive charge : 667.7820 centred at (gu) : 92.24258 81.89090 83.50018 assigned negative charge : -675.2853 centred at (gu) : 91.52448 82.09235 84.12460 start vw surface at 0.1700000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 233127 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33957 grid for indexing accessible points = 1.400000 m= 114615 mr = 176401 m= 35000 mr = 94121 m= 6641 mr = 27565 m= 536 mr = 4828 m= 11 mr = 315 m= 0 mr = 2 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 20859 time to turn everything in is 2.060000 number of dielectric boundary points 86698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 34121 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) : 1.688805 object centre at (A) : 3.802500 66.86400 61.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5042392 -0.2931907 midg,1,midg; midg,igrid,midg 0.3245996 -0.1104088 1,midg,midg; igrid,midg,midg -0.2999792 0.2042887 gauss-seidel spectral radius is 0.9992285 estimated iterations to convergence 284 setup time was (sec) 2.420000 now iterating at: 11:49:10 rms-change max change #iterations 11.29322 364.0639 at 10iterations 6.534113 165.7531 at 20iterations 3.774326 71.32310 at 30iterations 2.168051 39.34534 at 40iterations 1.241596 23.71750 at 50iterations 0.7103008 17.59321 at 60iterations 0.4056136 8.125274 at 70iterations 0.2314074 4.293663 at 80iterations 0.1321329 2.271399 at 90iterations 7.5261943E-02 1.265531 at 100iterations 4.2825766E-02 0.7251673 at 110iterations 2.4410818E-02 0.4020443 at 120iterations 1.3919842E-02 0.2388774 at 130iterations 7.9524713E-03 0.1271706 at 140iterations 4.5397556E-03 7.8945160E-02 at 150iterations 2.6081100E-03 4.1305542E-02 at 160iterations 1.5128853E-03 2.5833130E-02 at 170iterations 8.8635442E-04 1.6220093E-02 at 180iterations finished qdiffx linear iterations at : 11:49:28 total time elapsed so far: 20.62000 # loops : 180 mean,max change (kT/e) : 8.8635442E-04 1.6220093E-02 energy calculations done at 20.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.80000 DelPhi exited at 11:49:29 20.805u 0.478s 0:21.59 98.5% 0+0k 0+0io 0pf+0w