Tue Oct 11 06:39:28 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 06:39:29 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2056 !!! WARNING: SEP 190 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: 0.7099128 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): -19.97100 24.60400 ymin,ymax (A): -28.57900 12.07600 zmin,zma (A): -13.40600 36.74100 x,y,z range (A): 44.57500 40.65500 50.14700 scale (grids/A): 0.7099128 object centre (A): 2.316501 -8.251501 11.66750 number of atom coordinates read : 2056 total number of charged atoms : 1926 net assigned charge : 7.025010 assigned positive charge : 312.8891 centred at (gu) : 89.76395 90.23344 89.34171 assigned negative charge : -305.8641 centred at (gu) : 89.58467 90.20805 89.31931 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6980 nv = 96 ne = 84 npr = 41469 no. pairs analyzed = 41469 no. exposed pairs = 2473 no. arc points = 16949 no. surface atoms = 840 nbur = 1216 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 438 mr = 3997 m= 0 mr = 61 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1636 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7830 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8424202E-08 6.5936163E-08 midg,1,midg; midg,igrid,midg 4.8061008E-08 7.9614040E-08 1,midg,midg; igrid,midg,midg -3.1906723E-08 1.4652291E-07 gauss-seidel spectral radius is 0.9896527 estimated iterations to convergence 80 setup time was (sec) 0.4900000 now iterating at: 06:39:29 rms-change max change #iterations 0.1990550 35.50903 at 10iterations 2.5356464E-02 3.475452 at 20iterations 3.3584421E-03 0.4269791 at 30iterations 5.2435609E-04 6.7237854E-02 at 40iterations 1.2013190E-04 1.5529633E-02 at 50iterations finished qdiffx linear iterations at : 06:39:32 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.2013190E-04 1.5529633E-02 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 06:39:32 3.096u 0.156s 0:03.64 89.0% 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 Tue Oct 11 2011 at 06:39:32 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2056 !!! WARNING: SEP 190 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: 2.129739 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): -19.97100 24.60400 ymin,ymax (A): -28.57900 12.07600 zmin,zma (A): -13.40600 36.74100 x,y,z range (A): 44.57500 40.65500 50.14700 scale (grids/A): 2.129739 object centre (A): 2.316501 -8.251501 11.66750 number of atom coordinates read : 2056 total number of charged atoms : 1926 net assigned charge : 7.025010 assigned positive charge : 312.8891 centred at (gu) : 89.29205 90.70030 88.02523 assigned negative charge : -305.8641 centred at (gu) : 88.75395 90.62442 87.95782 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16949 grid for indexing accessible points = 1.400000 m= 29600 mr = 53137 m= 5694 mr = 22330 m= 499 mr = 3720 m= 12 mr = 252 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 30934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15322 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) : 0.7099128 object centre at (A) : 2.316501 -8.251501 11.66750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9206215E-02 4.0434945E-02 midg,1,midg; midg,igrid,midg 3.8059957E-03 3.0515192E-02 1,midg,midg; igrid,midg,midg 1.4804382E-02 3.9807435E-02 gauss-seidel spectral radius is 0.9988358 estimated iterations to convergence 232 setup time was (sec) 0.7900000 now iterating at: 06:39:33 rms-change max change #iterations 4.605259 183.0445 at 10iterations 2.279389 79.04071 at 20iterations 1.134200 37.75575 at 30iterations 0.5623935 16.56245 at 40iterations 0.2809704 8.466387 at 50iterations 0.1399346 4.224440 at 60iterations 6.9422409E-02 2.141045 at 70iterations 3.4578986E-02 1.123749 at 80iterations 1.7263360E-02 0.5255470 at 90iterations 8.6704018E-03 0.2622310 at 100iterations 4.3630712E-03 0.1388397 at 110iterations 2.2242647E-03 7.0986986E-02 at 120iterations finished qdiffx linear iterations at : 06:39:39 total time elapsed so far: 6.980000 # loops : 120 mean,max change (kT/e) : 2.2242647E-03 7.0986986E-02 energy calculations done at 6.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 06:39:40 7.161u 0.164s 0:07.82 93.6% 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 06:39:40 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2056 !!! WARNING: SEP 190 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: 3.194608 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): -19.97100 24.60400 ymin,ymax (A): -28.57900 12.07600 zmin,zma (A): -13.40600 36.74100 x,y,z range (A): 44.57500 40.65500 50.14700 scale (grids/A): 3.194608 object centre (A): 2.316501 -8.251501 11.66750 number of atom coordinates read : 2056 total number of charged atoms : 1926 net assigned charge : 7.025010 assigned positive charge : 312.8891 centred at (gu) : 88.93806 91.05042 87.03777 assigned negative charge : -305.8641 centred at (gu) : 88.13084 90.93662 86.93684 start vw surface at 0.1500000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 172017 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16949 grid for indexing accessible points = 1.400000 m= 92982 mr = 128017 m= 37491 mr = 77252 m= 10812 mr = 30708 m= 2081 mr = 8355 m= 231 mr = 1474 m= 5 mr = 148 m= 0 mr = 2 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.710000 number of dielectric boundary points 69663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 15408 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) : 2.129739 object centre at (A) : 2.316501 -8.251501 11.66750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7205279 0.3321009 midg,1,midg; midg,igrid,midg 1.8031664E-02 0.2322270 1,midg,midg; igrid,midg,midg 0.2609367 0.2959901 gauss-seidel spectral radius is 0.9992936 estimated iterations to convergence 297 setup time was (sec) 2.000000 now iterating at: 06:39:42 rms-change max change #iterations 10.21344 407.0076 at 10iterations 6.026282 142.4461 at 20iterations 3.557583 72.75289 at 30iterations 2.097732 41.00698 at 40iterations 1.231184 24.07395 at 50iterations 0.7225366 13.74170 at 60iterations 0.4236661 7.721274 at 70iterations 0.2485376 4.780066 at 80iterations 0.1457922 2.695274 at 90iterations 8.5294060E-02 1.609801 at 100iterations 5.0077032E-02 0.8155098 at 110iterations 2.9470863E-02 0.5121861 at 120iterations 1.7462889E-02 0.3176079 at 130iterations 1.0488655E-02 0.2031822 at 140iterations 6.4424807E-03 0.1302147 at 150iterations 4.0841838E-03 7.6850891E-02 at 160iterations 2.7242168E-03 5.2724838E-02 at 170iterations 1.9184877E-03 3.7170410E-02 at 180iterations finished qdiffx linear iterations at : 06:39:52 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 1.9184877E-03 3.7170410E-02 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 06:39:53 11.698u 0.206s 0:12.50 95.1% 0+0k 0+0io 0pf+0w