Sun Oct 9 16:30:21 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 16:30:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3006 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: 0.6148532 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): 8.356000 63.83400 ymin,ymax (A): -22.16700 35.73300 zmin,zma (A): -20.89700 32.52000 x,y,z range (A): 55.47800 57.90000 53.41700 scale (grids/A): 0.6148532 object centre (A): 36.09500 6.783001 5.811500 number of atom coordinates read : 3006 total number of charged atoms : 2928 net assigned charge : 2.000007 assigned positive charge : 458.1638 centred at (gu) : 90.14619 90.99500 91.35155 assigned negative charge : -456.1655 centred at (gu) : 90.04794 91.00916 91.24640 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7682 nv = 96 ne = 84 npr = 57930 no. pairs analyzed = 57930 no. exposed pairs = 4183 no. arc points = 29071 no. surface atoms = 1393 nbur = 1613 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 3892 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3200000 number of dielectric boundary points 4141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2869 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9526 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3128709E-09 1.1179331E-08 midg,1,midg; midg,igrid,midg 1.7857255E-09 3.7958844E-10 1,midg,midg; igrid,midg,midg -5.2128510E-09 8.0430125E-09 gauss-seidel spectral radius is 0.9863480 estimated iterations to convergence 70 setup time was (sec) 0.6000000 now iterating at: 16:30:22 rms-change max change #iterations 0.1310678 21.49359 at 10iterations 1.1785718E-02 1.727346 at 20iterations 1.1213339E-03 0.1559982 at 30iterations 1.4075027E-04 2.1395206E-02 at 40iterations 3.1839609E-05 5.4321289E-03 at 50iterations finished qdiffx linear iterations at : 16:30:26 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 3.1839609E-05 5.4321289E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 16:30:26 4.274u 0.247s 0:04.79 94.1% 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 16:30:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3006 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: 1.844560 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): 8.356000 63.83400 ymin,ymax (A): -22.16700 35.73300 zmin,zma (A): -20.89700 32.52000 x,y,z range (A): 55.47800 57.90000 53.41700 scale (grids/A): 1.844560 object centre (A): 36.09500 6.783001 5.811500 number of atom coordinates read : 3006 total number of charged atoms : 2928 net assigned charge : 2.000007 assigned positive charge : 458.1638 centred at (gu) : 90.43764 92.98434 94.05377 assigned negative charge : -456.1655 centred at (gu) : 90.14368 93.02708 93.73879 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 82100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29071 grid for indexing accessible points = 1.400000 m= 28795 mr = 54389 m= 4470 mr = 20260 m= 271 mr = 2740 m= 5 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 307 time to turn everything in is 0.7100000 number of dielectric boundary points 38175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 22890 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) : 0.6148532 object centre at (A) : 36.09500 6.783001 5.811500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7356679E-02 -3.7681274E-03 midg,1,midg; midg,igrid,midg 3.8774665E-02 3.1495847E-02 1,midg,midg; igrid,midg,midg -2.0709947E-02 -6.3637053E-03 gauss-seidel spectral radius is 0.9986002 estimated iterations to convergence 212 setup time was (sec) 1.050000 now iterating at: 16:30:27 rms-change max change #iterations 4.379932 166.1345 at 10iterations 2.029215 70.86245 at 20iterations 0.9429798 30.51526 at 30iterations 0.4380968 14.94754 at 40iterations 0.2029473 6.056009 at 50iterations 9.4315201E-02 3.376877 at 60iterations 4.3820903E-02 1.435565 at 70iterations 2.0292152E-02 0.6067381 at 80iterations 9.4337380E-03 0.2914419 at 90iterations 4.3895696E-03 0.1546164 at 100iterations 2.0367682E-03 6.2102318E-02 at 110iterations 9.4862061E-04 3.1510353E-02 at 120iterations finished qdiffx linear iterations at : 16:30:36 total time elapsed so far: 9.600000 # loops : 120 mean,max change (kT/e) : 9.4862061E-04 3.1510353E-02 energy calculations done at 9.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.780000 DelPhi exited at 16:30:36 9.784u 0.278s 0:10.34 97.1% 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 16:30:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3006 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: 2.766839 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): 8.356000 63.83400 ymin,ymax (A): -22.16700 35.73300 zmin,zma (A): -20.89700 32.52000 x,y,z range (A): 55.47800 57.90000 53.41700 scale (grids/A): 2.766839 object centre (A): 36.09500 6.783001 5.811500 number of atom coordinates read : 3006 total number of charged atoms : 2928 net assigned charge : 2.000007 assigned positive charge : 458.1638 centred at (gu) : 90.65624 94.47628 96.08060 assigned negative charge : -456.1655 centred at (gu) : 90.21552 94.54043 95.60804 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 190095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29071 grid for indexing accessible points = 1.400000 m= 92459 mr = 133178 m= 33139 mr = 73071 m= 7989 mr = 25914 m= 1031 mr = 5929 m= 54 mr = 670 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 1089 time to turn everything in is 1.610000 number of dielectric boundary points 85976 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 23420 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) : 1.844560 object centre at (A) : 36.09500 6.783001 5.811500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2316673 -0.1129322 midg,1,midg; midg,igrid,midg 0.3587731 0.4860851 1,midg,midg; igrid,midg,midg -0.2799424 -0.2541222 gauss-seidel spectral radius is 0.9992731 estimated iterations to convergence 293 setup time was (sec) 1.950000 now iterating at: 16:30:39 rms-change max change #iterations 10.58458 301.8622 at 10iterations 6.292768 155.8385 at 20iterations 3.716288 95.51836 at 30iterations 2.178102 42.10355 at 40iterations 1.271980 23.98113 at 50iterations 0.7420763 16.41672 at 60iterations 0.4316128 9.235020 at 70iterations 0.2505490 4.559654 at 80iterations 0.1454788 2.543010 at 90iterations 8.4218286E-02 1.424271 at 100iterations 4.8799265E-02 0.9263039 at 110iterations 2.8266143E-02 0.4821081 at 120iterations 1.6362889E-02 0.2923737 at 130iterations 9.4466200E-03 0.1684608 at 140iterations 5.4474557E-03 0.1034584 at 150iterations 3.1563931E-03 6.5136909E-02 at 160iterations 1.8245541E-03 3.3109665E-02 at 170iterations 1.0549956E-03 1.7638206E-02 at 180iterations finished qdiffx linear iterations at : 16:30:52 total time elapsed so far: 15.60000 # loops : 180 mean,max change (kT/e) : 1.0549956E-03 1.7638206E-02 energy calculations done at 15.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.77000 DelPhi exited at 16:30:53 15.770u 0.337s 0:16.38 98.2% 0+0k 0+0io 0pf+0w