Sat Oct 8 11:49:45 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 Sat Oct 8 2011 at 11:49:46 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIT 130 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5682544 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): -14.41700 35.89400 ymin,ymax (A): 30.82600 74.91700 zmin,zma (A): -11.18100 51.46700 x,y,z range (A): 50.31100 44.09100 62.64800 scale (grids/A): 0.5682544 object centre (A): 10.73850 52.87150 20.14300 number of atom coordinates read : 2587 total number of charged atoms : 2438 net assigned charge : -2.985991 assigned positive charge : 382.2635 centred at (gu) : 91.20831 90.77798 90.67530 assigned negative charge : -385.2503 centred at (gu) : 91.17733 90.78516 90.69938 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5466 nv = 96 ne = 84 npr = 52503 no. pairs analyzed = 52503 no. exposed pairs = 3328 no. arc points = 23571 no. surface atoms = 1126 nbur = 1461 mkacc time = 0.1300000 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 = 1.512000 m= 225 mr = 2787 m= 0 mr = 8 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2428 ## 301 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7048 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0830173E-10 -8.6865953E-10 midg,1,midg; midg,igrid,midg -2.8451844E-10 -6.2776573E-10 1,midg,midg; igrid,midg,midg -6.2399569E-10 -4.0787224E-11 gauss-seidel spectral radius is 0.9839925 estimated iterations to convergence 65 setup time was (sec) 0.5700000 now iterating at: 11:49:46 rms-change max change #iterations 8.2423650E-02 14.57917 at 10iterations 6.1532077E-03 0.9757624 at 20iterations 4.6054114E-04 7.4699402E-02 at 30iterations 3.4384164E-05 5.8631897E-03 at 40iterations 2.6803259E-06 4.5394897E-04 at 50iterations finished qdiffx linear iterations at : 11:49:50 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 2.6803259E-06 4.5394897E-04 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 11:49:51 4.615u 0.387s 0:05.34 93.4% 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 Sat Oct 8 2011 at 11:49:51 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIT 130 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.704763 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): -14.41700 35.89400 ymin,ymax (A): 30.82600 74.91700 zmin,zma (A): -11.18100 51.46700 x,y,z range (A): 50.31100 44.09100 62.64800 scale (grids/A): 1.704763 object centre (A): 10.73850 52.87150 20.14300 number of atom coordinates read : 2587 total number of charged atoms : 2438 net assigned charge : -2.985991 assigned positive charge : 382.2635 centred at (gu) : 93.62441 92.33327 92.02535 assigned negative charge : -385.2503 centred at (gu) : 93.53187 92.35517 92.09772 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 60115 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23571 grid for indexing accessible points = 1.400000 m= 18542 mr = 40185 m= 1828 mr = 12644 m= 42 mr = 896 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 26798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 18848 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) : 0.5682544 object centre at (A) : 10.73850 52.87150 20.14300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7557631E-03 -1.9214131E-02 midg,1,midg; midg,igrid,midg 2.1027215E-03 -4.6722651E-03 1,midg,midg; igrid,midg,midg -5.4793889E-03 3.6963765E-04 gauss-seidel spectral radius is 0.9982965 estimated iterations to convergence 192 setup time was (sec) 0.8100000 now iterating at: 11:49:52 rms-change max change #iterations 3.373023 148.8647 at 10iterations 1.433038 55.38133 at 20iterations 0.6144977 23.84853 at 30iterations 0.2625882 8.798946 at 40iterations 0.1125595 3.870319 at 50iterations 4.8282355E-02 1.956274 at 60iterations 2.0575205E-02 0.7638550 at 70iterations 8.8107986E-03 0.3518705 at 80iterations 3.7680108E-03 0.1437454 at 90iterations 1.6182200E-03 5.9019655E-02 at 100iterations 6.9399731E-04 2.4723053E-02 at 110iterations 2.9666637E-04 1.2363434E-02 at 120iterations finished qdiffx linear iterations at : 11:50:02 total time elapsed so far: 11.09000 # loops : 120 mean,max change (kT/e) : 2.9666637E-04 1.2363434E-02 energy calculations done at 11.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.27000 DelPhi exited at 11:50:03 11.271u 0.441s 0:12.03 97.3% 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 Sat Oct 8 2011 at 11:50:03 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIT 130 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.557145 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): -14.41700 35.89400 ymin,ymax (A): 30.82600 74.91700 zmin,zma (A): -11.18100 51.46700 x,y,z range (A): 50.31100 44.09100 62.64800 scale (grids/A): 2.557145 object centre (A): 10.73850 52.87150 20.14300 number of atom coordinates read : 2587 total number of charged atoms : 2438 net assigned charge : -2.985991 assigned positive charge : 382.2635 centred at (gu) : 95.43631 93.49969 93.03799 assigned negative charge : -385.2503 centred at (gu) : 95.29766 93.53271 93.14645 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 139707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23571 grid for indexing accessible points = 1.400000 m= 63392 mr = 98516 m= 18590 mr = 49942 m= 2822 mr = 13894 m= 175 mr = 1808 m= 4 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 60450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 19496 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) : 1.704763 object centre at (A) : 10.73850 52.87150 20.14300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2049285E-02 -1.9114941E-02 midg,1,midg; midg,igrid,midg 3.9214261E-02 -9.5530361E-02 1,midg,midg; igrid,midg,midg -7.0827343E-02 -2.8229482E-03 gauss-seidel spectral radius is 0.9991627 estimated iterations to convergence 273 setup time was (sec) 1.600000 now iterating at: 11:50:05 rms-change max change #iterations 8.441178 303.5651 at 10iterations 4.751285 125.6143 at 20iterations 2.656856 69.95377 at 30iterations 1.482337 36.76364 at 40iterations 0.8262264 22.55853 at 50iterations 0.4608454 10.68365 at 60iterations 0.2555393 5.767876 at 70iterations 0.1419671 3.127504 at 80iterations 7.8896366E-02 1.613446 at 90iterations 4.3825440E-02 1.038946 at 100iterations 2.4325080E-02 0.5596676 at 110iterations 1.3472861E-02 0.2883110 at 120iterations 7.4682604E-03 0.1606541 at 130iterations 4.1385596E-03 0.1028252 at 140iterations 2.2902349E-03 4.7235489E-02 at 150iterations 1.2670254E-03 2.7787685E-02 at 160iterations 7.0191629E-04 1.5816689E-02 at 170iterations 3.9022742E-04 8.3270073E-03 at 180iterations finished qdiffx linear iterations at : 11:50:21 total time elapsed so far: 17.94000 # loops : 180 mean,max change (kT/e) : 3.9022742E-04 8.3270073E-03 energy calculations done at 17.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.12000 DelPhi exited at 11:50:22 18.126u 0.475s 0:18.94 98.1% 0+0k 0+0io 0pf+0w