Tue Oct 11 08:29:44 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 Tue Oct 11 2011 at 08:29:44 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6600905 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): -26.33700 27.59500 ymin,ymax (A): -3.757000 48.90600 zmin,zma (A): -1.158000 51.62600 x,y,z range (A): 53.93200 52.66300 52.78400 scale (grids/A): 0.6600905 object centre (A): 0.6290007 22.57450 25.23400 number of atom coordinates read : 2809 total number of charged atoms : 2650 net assigned charge : 6.451015 assigned positive charge : 429.9547 centred at (gu) : 90.56111 91.99103 90.70959 assigned negative charge : -423.5042 centred at (gu) : 90.76471 91.88206 90.81227 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8039 nv = 96 ne = 84 npr = 57206 no. pairs analyzed = 57206 no. exposed pairs = 3337 no. arc points = 23495 no. surface atoms = 1124 nbur = 1685 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 503 mr = 4581 m= 5 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3300000 number of dielectric boundary points 3876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2195 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9537 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3027870E-08 -7.1322162E-09 midg,1,midg; midg,igrid,midg -4.5999036E-09 6.0089050E-08 1,midg,midg; igrid,midg,midg 5.2735793E-08 -3.2182658E-08 gauss-seidel spectral radius is 0.9881197 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 08:29:45 rms-change max change #iterations 0.1784735 25.09697 at 10iterations 1.9088954E-02 2.635808 at 20iterations 2.0340129E-03 0.3147697 at 30iterations 2.1974782E-04 3.1434059E-02 at 40iterations 2.4881792E-05 3.1433105E-03 at 50iterations finished qdiffx linear iterations at : 08:29:49 total time elapsed so far: 4.500000 # loops : 50 mean,max change (kT/e) : 2.4881792E-05 3.1433105E-03 energy calculations done at 4.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 08:29:50 4.672u 0.394s 0:05.42 93.3% 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 Tue Oct 11 2011 at 08:29:50 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.980271 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): -26.33700 27.59500 ymin,ymax (A): -3.757000 48.90600 zmin,zma (A): -1.158000 51.62600 x,y,z range (A): 53.93200 52.66300 52.78400 scale (grids/A): 1.980271 object centre (A): 0.6290007 22.57450 25.23400 number of atom coordinates read : 2809 total number of charged atoms : 2650 net assigned charge : 6.451015 assigned positive charge : 429.9547 centred at (gu) : 91.68282 95.97280 92.12839 assigned negative charge : -423.5042 centred at (gu) : 92.29385 95.64577 92.43679 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23495 grid for indexing accessible points = 1.400000 m= 32835 mr = 60591 m= 5587 mr = 24755 m= 394 mr = 3688 m= 10 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 690 time to turn everything in is 0.7100000 number of dielectric boundary points 35860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 20940 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) : 0.6600905 object centre at (A) : 0.6290007 22.57450 25.23400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6207397E-02 -6.5288390E-03 midg,1,midg; midg,igrid,midg 6.9204653E-03 5.2119825E-02 1,midg,midg; igrid,midg,midg 0.1001512 -3.3474304E-02 gauss-seidel spectral radius is 0.9987503 estimated iterations to convergence 224 setup time was (sec) 1.030000 now iterating at: 08:29:51 rms-change max change #iterations 4.881611 187.8402 at 10iterations 2.362165 64.77121 at 20iterations 1.140148 32.76710 at 30iterations 0.5552300 18.49109 at 40iterations 0.2696774 8.913677 at 50iterations 0.1310492 4.403240 at 60iterations 6.3212298E-02 1.720843 at 70iterations 3.0594321E-02 0.9262886 at 80iterations 1.4832980E-02 0.4570136 at 90iterations 7.1896459E-03 0.2004099 at 100iterations 3.4987736E-03 0.1105614 at 110iterations 1.6993911E-03 5.5801392E-02 at 120iterations finished qdiffx linear iterations at : 08:30:01 total time elapsed so far: 10.90000 # loops : 120 mean,max change (kT/e) : 1.6993911E-03 5.5801392E-02 energy calculations done at 10.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.08000 DelPhi exited at 08:30:02 11.082u 0.453s 0:12.15 94.8% 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 Tue Oct 11 2011 at 08:30:02 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.970407 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): -26.33700 27.59500 ymin,ymax (A): -3.757000 48.90600 zmin,zma (A): -1.158000 51.62600 x,y,z range (A): 53.93200 52.66300 52.78400 scale (grids/A): 2.970407 object centre (A): 0.6290007 22.57450 25.23400 number of atom coordinates read : 2809 total number of charged atoms : 2650 net assigned charge : 6.451015 assigned positive charge : 429.9547 centred at (gu) : 92.52421 98.95915 93.19224 assigned negative charge : -423.5042 centred at (gu) : 93.44064 98.46865 93.65508 start vw surface at 0.1200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 198946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23495 grid for indexing accessible points = 1.400000 m= 104418 mr = 145902 m= 39867 mr = 86676 m= 10429 mr = 32600 m= 1763 mr = 8066 m= 160 mr = 1312 m= 7 mr = 100 m= 0 mr = 1 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 2327 time to turn everything in is 1.900000 number of dielectric boundary points 80933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 21197 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) : 1.980271 object centre at (A) : 0.6290007 22.57450 25.23400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3045806 -8.4959425E-02 midg,1,midg; midg,igrid,midg 0.1524374 0.5433818 1,midg,midg; igrid,midg,midg 0.9188584 -0.3497283 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 2.220000 now iterating at: 08:30:05 rms-change max change #iterations 11.07566 372.3125 at 10iterations 6.512625 130.4280 at 20iterations 3.820278 73.80201 at 30iterations 2.235728 42.90015 at 40iterations 1.309007 24.75462 at 50iterations 0.7636221 13.83605 at 60iterations 0.4458487 8.560049 at 70iterations 0.2601165 4.598038 at 80iterations 0.1515101 2.694250 at 90iterations 8.8453524E-02 1.408142 at 100iterations 5.1474482E-02 0.8967838 at 110iterations 2.9990481E-02 0.4910382 at 120iterations 1.7451433E-02 0.3175735 at 130iterations 1.0174846E-02 0.1575069 at 140iterations 5.9346636E-03 9.9885941E-02 at 150iterations 3.4622597E-03 6.1693192E-02 at 160iterations 2.0243430E-03 3.3920288E-02 at 170iterations 1.1898046E-03 2.0481110E-02 at 180iterations finished qdiffx linear iterations at : 08:30:22 total time elapsed so far: 19.01000 # loops : 180 mean,max change (kT/e) : 1.1898046E-03 2.0481110E-02 energy calculations done at 19.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.18000 DelPhi exited at 08:30:22 19.184u 0.501s 0:20.23 97.2% 0+0k 0+0io 0pf+0w