Sun Oct 9 22:18:54 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 Sun Oct 9 2011 at 22:18:54 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: HIZ 560 has a net charge of 0.2000 !!! WARNING: ZN1 1551 has a net charge of 1.4000 !!! WARNING: ZN1 1555 has a net charge of 1.4000 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: 0.6638200 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): 16.77900 70.29600 ymin,ymax (A): -38.00600 15.62300 zmin,zma (A): -8.650000 43.81700 x,y,z range (A): 53.51700 53.62900 52.46700 scale (grids/A): 0.6638200 object centre (A): 43.53750 -11.19150 17.58350 number of atom coordinates read : 3133 total number of charged atoms : 2985 net assigned charge : 6.900014 assigned positive charge : 476.4238 centred at (gu) : 90.59142 88.55592 90.64295 assigned negative charge : -469.5252 centred at (gu) : 90.47789 88.49340 90.62553 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 9342 nv = 96 ne = 84 npr = 61868 no. pairs analyzed = 61868 no. exposed pairs = 4010 no. arc points = 28664 no. surface atoms = 1348 nbur = 1785 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 532 mr = 5030 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2400000 number of dielectric boundary points 4791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2771 ## 278 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 11044 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3098568E-08 2.7359908E-08 midg,1,midg; midg,igrid,midg 3.4673078E-09 2.6688397E-08 1,midg,midg; igrid,midg,midg -9.4047490E-09 5.5345534E-08 gauss-seidel spectral radius is 0.9882931 estimated iterations to convergence 75 setup time was (sec) 0.4300000 now iterating at: 22:18:55 rms-change max change #iterations 0.1916455 25.60926 at 10iterations 2.0427326E-02 2.656679 at 20iterations 2.2226386E-03 0.2713890 at 30iterations 2.3853236E-04 3.3939362E-02 at 40iterations 2.6699137E-05 3.0632019E-03 at 50iterations finished qdiffx linear iterations at : 22:18:58 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.6699137E-05 3.0632019E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 22:18:58 3.472u 0.172s 0:03.94 92.3% 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 Sun Oct 9 2011 at 22:18:58 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: HIZ 560 has a net charge of 0.2000 !!! WARNING: ZN1 1551 has a net charge of 1.4000 !!! WARNING: ZN1 1555 has a net charge of 1.4000 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: 1.991460 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): 16.77900 70.29600 ymin,ymax (A): -38.00600 15.62300 zmin,zma (A): -8.650000 43.81700 x,y,z range (A): 53.51700 53.62900 52.46700 scale (grids/A): 1.991460 object centre (A): 43.53750 -11.19150 17.58350 number of atom coordinates read : 3133 total number of charged atoms : 2985 net assigned charge : 6.900014 assigned positive charge : 476.4238 centred at (gu) : 91.77356 85.66746 91.92836 assigned negative charge : -469.5252 centred at (gu) : 91.43336 85.47995 91.87635 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 100660 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28664 grid for indexing accessible points = 1.400000 m= 36685 mr = 69057 m= 6277 mr = 26974 m= 438 mr = 3911 m= 3 mr = 190 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2124 time to turn everything in is 0.4900000 number of dielectric boundary points 43931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 23551 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) : 0.6638200 object centre at (A) : 43.53750 -11.19150 17.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8503646E-03 -1.9011075E-02 midg,1,midg; midg,igrid,midg 8.6637244E-02 4.8581131E-02 1,midg,midg; igrid,midg,midg 2.7043012E-03 4.0167239E-02 gauss-seidel spectral radius is 0.9988038 estimated iterations to convergence 229 setup time was (sec) 0.7100000 now iterating at: 22:18:59 rms-change max change #iterations 5.139912 201.1576 at 10iterations 2.529477 84.01053 at 20iterations 1.237433 33.25874 at 30iterations 0.6066834 18.47358 at 40iterations 0.2980032 8.349579 at 50iterations 0.1464595 3.971710 at 60iterations 7.1901761E-02 2.003769 at 70iterations 3.5305981E-02 0.9572330 at 80iterations 1.7369082E-02 0.5247803 at 90iterations 8.5181911E-03 0.2346048 at 100iterations 4.1810330E-03 0.1135960 at 110iterations 2.0636290E-03 5.9425354E-02 at 120iterations finished qdiffx linear iterations at : 22:19:07 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 2.0636290E-03 5.9425354E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 22:19:07 8.170u 0.200s 0:08.71 96.0% 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 Sun Oct 9 2011 at 22:19:07 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: HIZ 560 has a net charge of 0.2000 !!! WARNING: ZN1 1551 has a net charge of 1.4000 !!! WARNING: ZN1 1555 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.987190 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): 16.77900 70.29600 ymin,ymax (A): -38.00600 15.62300 zmin,zma (A): -8.650000 43.81700 x,y,z range (A): 53.51700 53.62900 52.46700 scale (grids/A): 2.987190 object centre (A): 43.53750 -11.19150 17.58350 number of atom coordinates read : 3133 total number of charged atoms : 2985 net assigned charge : 6.900014 assigned positive charge : 476.4238 centred at (gu) : 92.66020 83.50086 92.89233 assigned negative charge : -469.5252 centred at (gu) : 92.15000 83.21964 92.81446 start vw surface at 0.1000000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 232658 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28664 grid for indexing accessible points = 1.400000 m= 117347 mr = 167733 m= 43596 mr = 95460 m= 11331 mr = 34704 m= 1901 mr = 8512 m= 155 mr = 1396 m= 5 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 6872 time to turn everything in is 1.310000 number of dielectric boundary points 99095 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 23880 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) : 1.991460 object centre at (A) : 43.53750 -11.19150 17.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6407814E-02 -0.3599363 midg,1,midg; midg,igrid,midg 0.6545800 0.3949609 1,midg,midg; igrid,midg,midg 0.2300523 0.4917581 gauss-seidel spectral radius is 0.9993219 estimated iterations to convergence 303 setup time was (sec) 1.550000 now iterating at: 22:19:09 rms-change max change #iterations 11.92386 436.2029 at 10iterations 7.182544 159.0526 at 20iterations 4.297227 81.92580 at 30iterations 2.573710 58.62680 at 40iterations 1.531267 26.65303 at 50iterations 0.9113756 17.45650 at 60iterations 0.5403137 10.65038 at 70iterations 0.3205737 5.720675 at 80iterations 0.1895538 2.969453 at 90iterations 0.1122956 1.846229 at 100iterations 6.6325113E-02 1.050158 at 110iterations 3.9160814E-02 0.6119423 at 120iterations 2.3153028E-02 0.4031487 at 130iterations 1.3631319E-02 0.2540512 at 140iterations 8.0520408E-03 0.1353030 at 150iterations 4.7454904E-03 8.0765009E-02 at 160iterations 2.7955936E-03 4.3151855E-02 at 170iterations 1.6522226E-03 2.6165009E-02 at 180iterations finished qdiffx linear iterations at : 22:19:21 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 1.6522226E-03 2.6165009E-02 energy calculations done at 13.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.58000 DelPhi exited at 22:19:21 13.586u 0.224s 0:14.15 97.5% 0+0k 0+0io 0pf+0w