Sun Oct 9 11:26:15 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 Sun Oct 9 2011 at 11:26:15 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1879 !!! WARNING: HIT 177 has a net charge of 0.5140 !!! WARNING: HIT 181 has a net charge of 0.5140 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: 0.7475379 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): -1.324000 44.68600 ymin,ymax (A): -21.18500 23.85300 zmin,zma (A): -7.977000 39.64600 x,y,z range (A): 46.01000 45.03800 47.62300 scale (grids/A): 0.7475379 object centre (A): 21.68100 1.334000 15.83450 number of atom coordinates read : 1879 total number of charged atoms : 1743 net assigned charge : -6.471981 assigned positive charge : 280.9200 centred at (gu) : 89.71427 90.03489 89.81290 assigned negative charge : -287.3921 centred at (gu) : 89.70075 89.96021 89.67928 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7290 nv = 96 ne = 84 npr = 39475 no. pairs analyzed = 39475 no. exposed pairs = 2211 no. arc points = 15794 no. surface atoms = 754 nbur = 1125 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4141 m= 5 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 152 time to turn everything in is 0.1600000 number of dielectric boundary points 3565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1288 ## 104 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7546 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8726134E-07 6.0104184E-09 midg,1,midg; midg,igrid,midg -2.1224655E-07 -5.5193951E-08 1,midg,midg; igrid,midg,midg -1.5587358E-07 -1.1345953E-07 gauss-seidel spectral radius is 0.9906496 estimated iterations to convergence 84 setup time was (sec) 0.3700000 now iterating at: 11:26:16 rms-change max change #iterations 0.2577558 32.72564 at 10iterations 3.5270300E-02 4.906887 at 20iterations 4.7934675E-03 0.6463737 at 30iterations 6.6082698E-04 0.1072655 at 40iterations 9.0315305E-05 1.4221191E-02 at 50iterations finished qdiffx linear iterations at : 11:26:19 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 9.0315305E-05 1.4221191E-02 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 11:26:19 3.523u 0.181s 0:04.09 90.4% 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 Sun Oct 9 2011 at 11:26:19 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1879 !!! WARNING: HIT 177 has a net charge of 0.5140 !!! WARNING: HIT 181 has a net charge of 0.5140 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: 2.242614 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): -1.324000 44.68600 ymin,ymax (A): -21.18500 23.85300 zmin,zma (A): -7.977000 39.64600 x,y,z range (A): 46.01000 45.03800 47.62300 scale (grids/A): 2.242614 object centre (A): 21.68100 1.334000 15.83450 number of atom coordinates read : 1879 total number of charged atoms : 1743 net assigned charge : -6.471981 assigned positive charge : 280.9200 centred at (gu) : 89.14278 90.10493 89.43874 assigned negative charge : -287.3921 centred at (gu) : 89.10226 89.88081 89.03785 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76547 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15794 grid for indexing accessible points = 1.400000 m= 31395 mr = 53743 m= 6818 mr = 24157 m= 698 mr = 4637 m= 25 mr = 342 m= 0 mr = 1 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 4374 time to turn everything in is 0.3900000 number of dielectric boundary points 32603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 13890 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) : 0.7475379 object centre at (A) : 21.68100 1.334000 15.83450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1468789 -3.4674060E-02 midg,1,midg; midg,igrid,midg 1.6718222E-03 3.0252287E-02 1,midg,midg; igrid,midg,midg -5.2006043E-02 -3.9215777E-02 gauss-seidel spectral radius is 0.9989208 estimated iterations to convergence 241 setup time was (sec) 0.6300000 now iterating at: 11:26:20 rms-change max change #iterations 4.936228 218.2463 at 10iterations 2.501243 82.45623 at 20iterations 1.271638 39.73909 at 30iterations 0.6501509 19.64605 at 40iterations 0.3309290 9.179351 at 50iterations 0.1684306 4.984589 at 60iterations 8.5815638E-02 2.378046 at 70iterations 4.3740243E-02 1.248909 at 80iterations 2.2277405E-02 0.6457558 at 90iterations 1.1368821E-02 0.3594170 at 100iterations 5.7731569E-03 0.1749001 at 110iterations 2.9482096E-03 9.1156006E-02 at 120iterations finished qdiffx linear iterations at : 11:26:28 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 2.9482096E-03 9.1156006E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 11:26:28 8.197u 0.219s 0:08.76 95.8% 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 Sun Oct 9 2011 at 11:26:28 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1879 !!! WARNING: HIT 177 has a net charge of 0.5140 !!! WARNING: HIT 181 has a net charge of 0.5140 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: 3.363921 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): -1.324000 44.68600 ymin,ymax (A): -21.18500 23.85300 zmin,zma (A): -7.977000 39.64600 x,y,z range (A): 46.01000 45.03800 47.62300 scale (grids/A): 3.363921 object centre (A): 21.68100 1.334000 15.83450 number of atom coordinates read : 1879 total number of charged atoms : 1743 net assigned charge : -6.471981 assigned positive charge : 280.9200 centred at (gu) : 88.71428 90.15755 89.15818 assigned negative charge : -287.3921 centred at (gu) : 88.65337 89.82130 88.55678 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 176123 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15794 grid for indexing accessible points = 1.400000 m= 95659 mr = 129134 m= 41766 mr = 80217 m= 13202 mr = 34620 m= 2860 mr = 10341 m= 348 mr = 2078 m= 15 mr = 208 m= 0 mr = 1 time to grow re-entrant surface = 0.6100001 no. cavity mid-points inaccessible to solvent = 15443 time to turn everything in is 1.230000 number of dielectric boundary points 73374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 13944 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) : 2.242614 object centre at (A) : 21.68100 1.334000 15.83450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.388187 -0.2393058 midg,1,midg; midg,igrid,midg 6.1695989E-02 0.2713622 1,midg,midg; igrid,midg,midg -0.3667514 -0.3575531 gauss-seidel spectral radius is 0.9993152 estimated iterations to convergence 301 setup time was (sec) 1.470000 now iterating at: 11:26:30 rms-change max change #iterations 10.61700 309.4117 at 10iterations 6.288363 135.5634 at 20iterations 3.706615 70.46847 at 30iterations 2.179739 36.98531 at 40iterations 1.281095 27.14062 at 50iterations 0.7552174 12.33144 at 60iterations 0.4437831 8.156903 at 70iterations 0.2607172 4.412800 at 80iterations 0.1532500 2.893806 at 90iterations 8.9718685E-02 1.462244 at 100iterations 5.2712832E-02 0.8536530 at 110iterations 3.0956544E-02 0.5051384 at 120iterations 1.8206969E-02 0.3354111 at 130iterations 1.0693743E-02 0.1822662 at 140iterations 6.2615355E-03 0.1040649 at 150iterations 3.6834138E-03 6.0897827E-02 at 160iterations 2.1556814E-03 3.6939621E-02 at 170iterations 1.2680778E-03 2.0337582E-02 at 180iterations finished qdiffx linear iterations at : 11:26:42 total time elapsed so far: 13.55000 # loops : 180 mean,max change (kT/e) : 1.2680778E-03 2.0337582E-02 energy calculations done at 13.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.68000 DelPhi exited at 11:26:42 13.684u 0.224s 0:14.22 97.7% 0+0k 0+0io 0pf+0w