Mon Oct 10 17:02:26 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 Mon Oct 10 2011 at 17:02:27 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4632 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5133234 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): -15.75200 36.13400 ymin,ymax (A): -30.02400 31.46000 zmin,zma (A): -4.332000 65.02000 x,y,z range (A): 51.88600 61.48400 69.35200 scale (grids/A): 0.5133234 object centre (A): 10.19100 0.7179995 30.34400 number of atom coordinates read : 4632 total number of charged atoms : 4426 net assigned charge : 6.306048 assigned positive charge : 696.2646 centred at (gu) : 89.86069 90.79720 88.36829 assigned negative charge : -689.9631 centred at (gu) : 89.78365 90.86329 88.38871 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7512 nv = 96 ne = 84 npr = 95408 no. pairs analyzed = 95408 no. exposed pairs = 5769 no. arc points = 39667 no. surface atoms = 1935 nbur = 2697 mkacc time = 0.2200000 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 = 1.652000 m= 262 mr = 3874 m= 0 mr = 4 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 3896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3937 ## 593 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 10261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4325097E-10 3.0027043E-11 midg,1,midg; midg,igrid,midg 2.3172735E-10 -1.0669809E-10 1,midg,midg; igrid,midg,midg -1.2109874E-10 3.0409072E-10 gauss-seidel spectral radius is 0.9805751 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 17:02:28 rms-change max change #iterations 7.0552275E-02 11.90137 at 10iterations 4.0983302E-03 0.7060204 at 20iterations 3.8946801E-04 5.4004669E-02 at 30iterations 1.2182398E-04 1.8337727E-02 at 40iterations 4.7919333E-05 7.1110725E-03 at 50iterations finished qdiffx linear iterations at : 17:02:30 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 4.7919333E-05 7.1110725E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 17:02:31 3.613u 0.159s 0:04.96 75.8% 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 Mon Oct 10 2011 at 17:02:32 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4632 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.539970 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): -15.75200 36.13400 ymin,ymax (A): -30.02400 31.46000 zmin,zma (A): -4.332000 65.02000 x,y,z range (A): 51.88600 61.48400 69.35200 scale (grids/A): 1.539970 object centre (A): 10.19100 0.7179995 30.34400 number of atom coordinates read : 4632 total number of charged atoms : 4426 net assigned charge : 6.306048 assigned positive charge : 696.2646 centred at (gu) : 89.58073 92.38989 85.10332 assigned negative charge : -689.9631 centred at (gu) : 89.35044 92.58958 85.16592 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 85693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39667 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 23777 mr = 58813 m= 2062 mr = 15429 m= 40 mr = 833 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 36497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 556 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 33413 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) : 0.5133234 object centre at (A) : 10.19100 0.7179995 30.34400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8359304E-03 -2.2248682E-03 midg,1,midg; midg,igrid,midg 1.1010122E-02 -6.7185881E-03 1,midg,midg; igrid,midg,midg 4.7364727E-05 8.6742621E-03 gauss-seidel spectral radius is 0.9981149 estimated iterations to convergence 183 setup time was (sec) 0.9300000 now iterating at: 17:02:33 rms-change max change #iterations 3.757111 145.2766 at 10iterations 1.541407 49.93832 at 20iterations 0.6313778 20.21157 at 30iterations 0.2594295 8.364271 at 40iterations 0.1065304 3.715021 at 50iterations 4.3852448E-02 1.426508 at 60iterations 1.8011408E-02 0.6175823 at 70iterations 7.4270461E-03 0.2403679 at 80iterations 3.1012390E-03 9.9641800E-02 at 90iterations 1.3073996E-03 4.0824652E-02 at 100iterations 5.7827629E-04 1.9577026E-02 at 110iterations 2.8186664E-04 1.0796547E-02 at 120iterations finished qdiffx linear iterations at : 17:02:40 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 2.8186664E-04 1.0796547E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 17:02:41 8.067u 0.184s 0:09.00 91.5% 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 Mon Oct 10 2011 at 17:02:41 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4632 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.309955 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): -15.75200 36.13400 ymin,ymax (A): -30.02400 31.46000 zmin,zma (A): -4.332000 65.02000 x,y,z range (A): 51.88600 61.48400 69.35200 scale (grids/A): 2.309955 object centre (A): 10.19100 0.7179995 30.34400 number of atom coordinates read : 4632 total number of charged atoms : 4426 net assigned charge : 6.306048 assigned positive charge : 696.2646 centred at (gu) : 89.37078 93.58455 82.65474 assigned negative charge : -689.9631 centred at (gu) : 89.02556 93.88416 82.74883 start vw surface at 0.2300000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 199889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39667 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 86483 mr = 144746 m= 21121 mr = 66970 m= 2893 mr = 14734 m= 136 mr = 1677 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.540000 number of dielectric boundary points 82361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 35325 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) : 1.539970 object centre at (A) : 10.19100 0.7179995 30.34400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1490246 -0.1468897 midg,1,midg; midg,igrid,midg 0.1727740 -0.1893536 1,midg,midg; igrid,midg,midg 3.4421277E-03 0.1337867 gauss-seidel spectral radius is 0.9991587 estimated iterations to convergence 272 setup time was (sec) 1.850000 now iterating at: 17:02:43 rms-change max change #iterations 10.14205 270.2779 at 10iterations 5.795185 147.3444 at 20iterations 3.284117 74.95547 at 30iterations 1.852412 39.30205 at 40iterations 1.042756 22.48729 at 50iterations 0.5850825 12.43120 at 60iterations 0.3272628 7.155869 at 70iterations 0.1825218 3.509174 at 80iterations 0.1019454 2.060314 at 90iterations 5.6766260E-02 1.061546 at 100iterations 3.1615749E-02 0.5772076 at 110iterations 1.7595371E-02 0.3782616 at 120iterations 9.7740339E-03 0.1920052 at 130iterations 5.4453979E-03 0.1078568 at 140iterations 3.0349207E-03 5.8784485E-02 at 150iterations 1.6971207E-03 3.4848213E-02 at 160iterations 9.5429819E-04 1.7876625E-02 at 170iterations 5.4614560E-04 1.0684967E-02 at 180iterations finished qdiffx linear iterations at : 17:02:53 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 5.4614560E-04 1.0684967E-02 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 17:02:54 12.579u 0.182s 0:13.07 97.5% 0+0k 0+0io 0pf+0w