Mon Oct 10 14:20:01 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 Mon Oct 10 2011 at 14:20:01 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5937985 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): -7.569000 44.06400 ymin,ymax (A): 13.27400 73.22700 zmin,zma (A): 54.62000 106.2010 x,y,z range (A): 51.63300 59.95300 51.58100 scale (grids/A): 0.5937985 object centre (A): 18.24750 43.25050 80.41051 number of atom coordinates read : 2594 total number of charged atoms : 2436 net assigned charge : -0.9999923 assigned positive charge : 385.4090 centred at (gu) : 90.12208 90.72889 89.58257 assigned negative charge : -386.4094 centred at (gu) : 89.93840 90.63058 89.61285 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6007 nv = 96 ne = 84 npr = 52591 no. pairs analyzed = 52591 no. exposed pairs = 3435 no. arc points = 23976 no. surface atoms = 1164 nbur = 1430 mkacc time = 0.1500000 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 = 1.456000 m= 276 mr = 3025 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2409 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7554 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8067645E-10 -1.1692339E-09 midg,1,midg; midg,igrid,midg -2.8332452E-09 3.0054372E-09 1,midg,midg; igrid,midg,midg -5.8260672E-09 5.1477662E-09 gauss-seidel spectral radius is 0.9853266 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 14:20:02 rms-change max change #iterations 0.1013277 18.67632 at 10iterations 8.2883183E-03 1.236076 at 20iterations 6.9857860E-04 0.1203098 at 30iterations 5.7253201E-05 9.9248886E-03 at 40iterations 4.8765169E-06 8.2778931E-04 at 50iterations finished qdiffx linear iterations at : 14:20:05 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 4.8765169E-06 8.2778931E-04 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 14:20:06 4.304u 0.227s 0:04.91 92.0% 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 Mon Oct 10 2011 at 14:20:06 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.781396 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): -7.569000 44.06400 ymin,ymax (A): 13.27400 73.22700 zmin,zma (A): 54.62000 106.2010 x,y,z range (A): 51.63300 59.95300 51.58100 scale (grids/A): 1.781396 object centre (A): 18.24750 43.25050 80.41051 number of atom coordinates read : 2594 total number of charged atoms : 2436 net assigned charge : -0.9999923 assigned positive charge : 385.4090 centred at (gu) : 90.36558 92.18604 88.74741 assigned negative charge : -386.4094 centred at (gu) : 89.81487 91.89169 88.83817 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 65781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23976 grid for indexing accessible points = 1.400000 m= 20811 mr = 43961 m= 2431 mr = 14061 m= 116 mr = 1098 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 177 time to turn everything in is 0.6500000 number of dielectric boundary points 29994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 18978 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) : 0.5937985 object centre at (A) : 18.24750 43.25050 80.41051 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3875071E-03 1.7467124E-04 midg,1,midg; midg,igrid,midg 1.5137305E-03 8.5492134E-03 1,midg,midg; igrid,midg,midg -2.7759330E-02 4.9767024E-03 gauss-seidel spectral radius is 0.9984424 estimated iterations to convergence 201 setup time was (sec) 1.050000 now iterating at: 14:20:07 rms-change max change #iterations 3.711574 163.6059 at 10iterations 1.632582 57.38231 at 20iterations 0.7259994 26.61704 at 30iterations 0.3229648 11.35184 at 40iterations 0.1430862 5.312365 at 50iterations 6.3474067E-02 2.181657 at 60iterations 2.8226260E-02 0.9529099 at 70iterations 1.2568400E-02 0.4262810 at 80iterations 5.5887895E-03 0.1871338 at 90iterations 2.4850604E-03 8.8785172E-02 at 100iterations 1.1031070E-03 3.7491798E-02 at 110iterations 4.9175625E-04 2.0063877E-02 at 120iterations finished qdiffx linear iterations at : 14:20:16 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 4.9175625E-04 2.0063877E-02 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.680000 DelPhi exited at 14:20:17 9.685u 0.260s 0:10.36 95.9% 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 14:20:17 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 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: 2.672093 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): -7.569000 44.06400 ymin,ymax (A): 13.27400 73.22700 zmin,zma (A): 54.62000 106.2010 x,y,z range (A): 51.63300 59.95300 51.58100 scale (grids/A): 2.672093 object centre (A): 18.24750 43.25050 80.41051 number of atom coordinates read : 2594 total number of charged atoms : 2436 net assigned charge : -0.9999923 assigned positive charge : 385.4090 centred at (gu) : 90.54822 93.27896 88.12097 assigned negative charge : -386.4094 centred at (gu) : 89.72224 92.83739 88.25716 start vw surface at 0.2100000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 152749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23976 grid for indexing accessible points = 1.400000 m= 70471 mr = 107699 m= 21445 mr = 55281 m= 3900 mr = 15802 m= 403 mr = 2333 m= 17 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 583 time to turn everything in is 1.590000 number of dielectric boundary points 67689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 19484 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) : 1.781396 object centre at (A) : 18.24750 43.25050 80.41051 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2139666 2.4895459E-02 midg,1,midg; midg,igrid,midg 1.4031913E-02 5.0662020E-03 1,midg,midg; igrid,midg,midg -0.3814052 1.2943432E-02 gauss-seidel spectral radius is 0.9992106 estimated iterations to convergence 281 setup time was (sec) 1.980000 now iterating at: 14:20:19 rms-change max change #iterations 9.079194 287.8689 at 10iterations 5.250739 140.2205 at 20iterations 2.995064 71.01318 at 30iterations 1.710953 42.72603 at 40iterations 0.9748882 20.32693 at 50iterations 0.5533173 12.67511 at 60iterations 0.3134066 7.498554 at 70iterations 0.1766944 3.676538 at 80iterations 0.1001862 2.121265 at 90iterations 5.6741439E-02 1.271044 at 100iterations 3.2018639E-02 0.6431274 at 110iterations 1.8072132E-02 0.3791504 at 120iterations 1.0210437E-02 0.2272911 at 130iterations 5.7560066E-03 0.1300468 at 140iterations 3.2493474E-03 6.6383362E-02 at 150iterations 1.8280450E-03 3.7277281E-02 at 160iterations 1.0310281E-03 2.1624088E-02 at 170iterations 5.8276206E-04 1.1562347E-02 at 180iterations finished qdiffx linear iterations at : 14:20:32 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 5.8276206E-04 1.1562347E-02 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.65000 DelPhi exited at 14:20:33 15.649u 0.277s 0:16.46 96.6% 0+0k 0+0io 0pf+0w