Sun Oct 9 07:25:19 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 Sun Oct 9 2011 at 07:25:19 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1683 !!! WARNING: NAP 164 has a net charge of -2.3370 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: 0.7283888 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): -7.407000 34.70200 ymin,ymax (A): -2.452000 40.09200 zmin,zma (A): -13.21700 35.65800 x,y,z range (A): 42.10900 42.54400 48.87500 scale (grids/A): 0.7283888 object centre (A): 13.64750 18.82000 11.22050 number of atom coordinates read : 1683 total number of charged atoms : 1546 net assigned charge : -11.83699 assigned positive charge : 250.3672 centred at (gu) : 91.06446 89.53499 90.20782 assigned negative charge : -262.2041 centred at (gu) : 90.91971 89.89933 90.31959 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6183 nv = 96 ne = 84 npr = 35322 no. pairs analyzed = 35322 no. exposed pairs = 2081 no. arc points = 14926 no. surface atoms = 709 nbur = 974 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 3531 m= 2 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 150 time to turn everything in is 0.2200000 number of dielectric boundary points 3000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1201 ## 66 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6499 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.7522089E-08 -2.4631652E-07 midg,1,midg; midg,igrid,midg 7.4299805E-08 -3.7536523E-07 1,midg,midg; igrid,midg,midg -2.1249279E-07 -8.3342627E-08 gauss-seidel spectral radius is 0.9901378 estimated iterations to convergence 82 setup time was (sec) 0.4300000 now iterating at: 07:25:20 rms-change max change #iterations 0.2079604 26.63646 at 10iterations 2.8193630E-02 4.280400 at 20iterations 3.6072675E-03 0.4844208 at 30iterations 4.6370114E-04 6.8662643E-02 at 40iterations 6.1401057E-05 8.8394880E-03 at 50iterations finished qdiffx linear iterations at : 07:25:22 total time elapsed so far: 2.830000 # loops : 50 mean,max change (kT/e) : 6.1401057E-05 8.8394880E-03 energy calculations done at 2.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.990000 DelPhi exited at 07:25:23 2.996u 0.140s 0:03.40 92.0% 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 07:25:23 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1683 !!! WARNING: NAP 164 has a net charge of -2.3370 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: 2.185166 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): -7.407000 34.70200 ymin,ymax (A): -2.452000 40.09200 zmin,zma (A): -13.21700 35.65800 x,y,z range (A): 42.10900 42.54400 48.87500 scale (grids/A): 2.185166 object centre (A): 13.64750 18.82000 11.22050 number of atom coordinates read : 1683 total number of charged atoms : 1546 net assigned charge : -11.83699 assigned positive charge : 250.3672 centred at (gu) : 93.19387 88.60497 90.62347 assigned negative charge : -262.2041 centred at (gu) : 92.75902 89.69806 90.95885 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 64838 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14926 grid for indexing accessible points = 1.400000 m= 26582 mr = 44942 m= 5462 mr = 20617 m= 597 mr = 3931 m= 26 mr = 379 m= 0 mr = 7 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3967 time to turn everything in is 0.4700000 number of dielectric boundary points 27629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 12321 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) : 0.7283888 object centre at (A) : 13.64750 18.82000 11.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5916551E-02 -8.1927747E-02 midg,1,midg; midg,igrid,midg 1.2104756E-02 -0.1070729 1,midg,midg; igrid,midg,midg -6.6586159E-02 -2.7013559E-02 gauss-seidel spectral radius is 0.9988555 estimated iterations to convergence 234 setup time was (sec) 0.7300000 now iterating at: 07:25:23 rms-change max change #iterations 4.488186 196.3356 at 10iterations 2.223679 84.42818 at 20iterations 1.116298 34.96066 at 30iterations 0.5533628 16.77102 at 40iterations 0.2772562 8.574707 at 50iterations 0.1383301 4.504368 at 60iterations 6.8908744E-02 2.157389 at 70iterations 3.4398537E-02 1.145882 at 80iterations 1.7191753E-02 0.5755887 at 90iterations 8.5468730E-03 0.2634888 at 100iterations 4.2851684E-03 0.1481323 at 110iterations 2.1399003E-03 7.1453094E-02 at 120iterations finished qdiffx linear iterations at : 07:25:29 total time elapsed so far: 6.650000 # loops : 120 mean,max change (kT/e) : 2.1399003E-03 7.1453094E-02 energy calculations done at 6.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.820000 DelPhi exited at 07:25:30 6.820u 0.160s 0:07.25 96.2% 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 07:25:30 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1683 !!! WARNING: NAP 164 has a net charge of -2.3370 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: 3.277750 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): -7.407000 34.70200 ymin,ymax (A): -2.452000 40.09200 zmin,zma (A): -13.21700 35.65800 x,y,z range (A): 42.10900 42.54400 48.87500 scale (grids/A): 3.277750 object centre (A): 13.64750 18.82000 11.22050 number of atom coordinates read : 1683 total number of charged atoms : 1546 net assigned charge : -11.83699 assigned positive charge : 250.3672 centred at (gu) : 94.79077 87.90755 90.93512 assigned negative charge : -262.2041 centred at (gu) : 94.13856 89.54709 91.43833 start vw surface at 0.1200000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 149098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14926 grid for indexing accessible points = 1.400000 m= 80848 mr = 107679 m= 35302 mr = 67956 m= 10671 mr = 30002 m= 2319 mr = 8566 m= 380 mr = 1820 m= 26 mr = 310 m= 0 mr = 11 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 13617 time to turn everything in is 1.470000 number of dielectric boundary points 62300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 12368 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) : 2.185166 object centre at (A) : 13.64750 18.82000 11.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1290141 -0.7193183 midg,1,midg; midg,igrid,midg 0.1570866 -0.7447369 1,midg,midg; igrid,midg,midg -0.4897193 -0.1792504 gauss-seidel spectral radius is 0.9992935 estimated iterations to convergence 297 setup time was (sec) 1.740000 now iterating at: 07:25:32 rms-change max change #iterations 9.829887 400.1381 at 10iterations 5.701582 142.0283 at 20iterations 3.320369 68.72710 at 30iterations 1.933147 38.26251 at 40iterations 1.122763 24.67069 at 50iterations 0.6526247 11.96027 at 60iterations 0.3795420 7.101680 at 70iterations 0.2205979 4.172713 at 80iterations 0.1276118 2.386005 at 90iterations 7.4363209E-02 1.370725 at 100iterations 4.3205250E-02 0.8474526 at 110iterations 2.5100049E-02 0.4453945 at 120iterations 1.4609720E-02 0.2722330 at 130iterations 8.4726829E-03 0.1508865 at 140iterations 4.9198838E-03 9.0667725E-02 at 150iterations 2.8614628E-03 4.9880028E-02 at 160iterations 1.6652476E-03 2.8472424E-02 at 170iterations 9.6749450E-04 1.7589569E-02 at 180iterations finished qdiffx linear iterations at : 07:25:41 total time elapsed so far: 11.10000 # loops : 180 mean,max change (kT/e) : 9.6749450E-04 1.7589569E-02 energy calculations done at 11.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.27000 DelPhi exited at 07:25:42 11.271u 0.181s 0:11.72 97.6% 0+0k 0+0io 0pf+0w