Sat Oct 8 12:51:45 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+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 Sat Oct 8 2011 at 12:51:45 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1304 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7029877 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): 0.3830000 40.44200 ymin,ymax (A): -4.387000 35.88000 zmin,zma (A): -15.78100 34.86000 x,y,z range (A): 40.05900 40.26700 50.64100 scale (grids/A): 0.7029877 object centre (A): 20.41250 15.74650 9.539500 number of atom coordinates read : 1304 total number of charged atoms : 1164 net assigned charge : 1.000011 assigned positive charge : 191.4982 centred at (gu) : 90.61278 89.00284 90.58663 assigned negative charge : -190.4980 centred at (gu) : 90.70287 88.85574 90.08296 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4445 nv = 96 ne = 84 npr = 25887 no. pairs analyzed = 25887 no. exposed pairs = 1688 no. arc points = 12458 no. surface atoms = 566 nbur = 738 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 270 mr = 2271 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1012 ## 81 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 4620 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2162229E-07 1.5568729E-07 midg,1,midg; midg,igrid,midg -4.0488747E-08 3.8814971E-08 1,midg,midg; igrid,midg,midg 2.8432696E-08 -1.9384837E-08 gauss-seidel spectral radius is 0.9893864 estimated iterations to convergence 79 setup time was (sec) 0.4600000 now iterating at: 12:51:46 rms-change max change #iterations 0.1524802 33.45883 at 10iterations 1.7748279E-02 3.071563 at 20iterations 2.1615289E-03 0.3661232 at 30iterations 2.5857551E-04 4.7569275E-02 at 40iterations 3.0203768E-05 5.6324005E-03 at 50iterations finished qdiffx linear iterations at : 12:51:49 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 3.0203768E-05 5.6324005E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 12:51:50 4.126u 0.230s 0:04.65 93.5% 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 12:51:50 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1304 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.108963 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): 0.3830000 40.44200 ymin,ymax (A): -4.387000 35.88000 zmin,zma (A): -15.78100 34.86000 x,y,z range (A): 40.05900 40.26700 50.64100 scale (grids/A): 2.108963 object centre (A): 20.41250 15.74650 9.539500 number of atom coordinates read : 1304 total number of charged atoms : 1164 net assigned charge : 1.000011 assigned positive charge : 191.4982 centred at (gu) : 91.83880 87.00883 91.76014 assigned negative charge : -190.4980 centred at (gu) : 92.10862 86.56715 90.24883 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 46641 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12458 grid for indexing accessible points = 1.400000 m= 16413 mr = 30526 m= 3099 mr = 11680 m= 311 mr = 2028 m= 7 mr = 180 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 22055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9243 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) : 0.7029877 object centre at (A) : 20.41250 15.74650 9.539500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7125893E-02 9.0940535E-02 midg,1,midg; midg,igrid,midg -2.5909433E-02 9.9896947E-03 1,midg,midg; igrid,midg,midg 5.5088178E-04 -2.5450503E-03 gauss-seidel spectral radius is 0.9987472 estimated iterations to convergence 224 setup time was (sec) 0.7100000 now iterating at: 12:51:51 rms-change max change #iterations 3.553646 209.9420 at 10iterations 1.694834 76.28765 at 20iterations 0.8173796 32.55578 at 30iterations 0.3945558 15.53668 at 40iterations 0.1899414 6.910566 at 50iterations 9.1554761E-02 3.743967 at 60iterations 4.4129521E-02 1.618439 at 70iterations 2.1191860E-02 0.8355865 at 80iterations 1.0232256E-02 0.3817997 at 90iterations 4.9299323E-03 0.1922722 at 100iterations 2.3865998E-03 9.6401215E-02 at 110iterations 1.1483079E-03 4.3951988E-02 at 120iterations finished qdiffx linear iterations at : 12:51:59 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 1.1483079E-03 4.3951988E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 12:52:00 9.388u 0.292s 0:09.97 96.9% 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 12:52:00 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1304 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.163445 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): 0.3830000 40.44200 ymin,ymax (A): -4.387000 35.88000 zmin,zma (A): -15.78100 34.86000 x,y,z range (A): 40.05900 40.26700 50.64100 scale (grids/A): 3.163445 object centre (A): 20.41250 15.74650 9.539500 number of atom coordinates read : 1304 total number of charged atoms : 1164 net assigned charge : 1.000011 assigned positive charge : 191.4982 centred at (gu) : 92.75831 85.51326 92.64017 assigned negative charge : -190.4980 centred at (gu) : 93.16296 84.85074 90.37323 start vw surface at 0.1100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 107416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12458 grid for indexing accessible points = 1.400000 m= 52458 mr = 73995 m= 19724 mr = 41913 m= 5794 mr = 15607 m= 1226 mr = 4414 m= 173 mr = 935 m= 3 mr = 120 m= 0 mr = 2 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 49808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 9312 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) : 2.108963 object centre at (A) : 20.41250 15.74650 9.539500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1162701 0.9317305 midg,1,midg; midg,igrid,midg -0.2684663 0.1028318 1,midg,midg; igrid,midg,midg -7.0355562E-03 -7.4248766E-03 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.520000 now iterating at: 12:52:02 rms-change max change #iterations 7.919720 349.3308 at 10iterations 4.524577 105.8849 at 20iterations 2.601989 59.61314 at 30iterations 1.495953 36.23912 at 40iterations 0.8572271 19.21187 at 50iterations 0.4928289 10.42732 at 60iterations 0.2830347 7.076598 at 70iterations 0.1624957 3.447838 at 80iterations 9.3236409E-02 2.297855 at 90iterations 5.3512763E-02 1.298290 at 100iterations 3.0752145E-02 0.6665406 at 110iterations 1.7659102E-02 0.3629322 at 120iterations 1.0146661E-02 0.2125502 at 130iterations 5.8328966E-03 0.1200342 at 140iterations 3.3540551E-03 7.2946548E-02 at 150iterations 1.9264206E-03 4.1866302E-02 at 160iterations 1.1079634E-03 2.6958466E-02 at 170iterations 6.3573697E-04 1.3603210E-02 at 180iterations finished qdiffx linear iterations at : 12:52:15 total time elapsed so far: 14.91000 # loops : 180 mean,max change (kT/e) : 6.3573697E-04 1.3603210E-02 energy calculations done at 14.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.09000 DelPhi exited at 12:52:15 15.089u 0.282s 0:15.64 98.2% 0+0k 0+0io 0pf+0w