Sat Oct 8 11:45:24 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 11:45:24 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4447 !!! WARNING: SEP 283 has a net charge of -0.4750 !!! WARNING: HIT 437 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5295807 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): 59.16500 114.6770 ymin,ymax (A): 19.09800 86.32100 zmin,zma (A): -7.708000 55.57300 x,y,z range (A): 55.51200 67.22300 63.28100 scale (grids/A): 0.5295807 object centre (A): 86.92100 52.70950 23.93250 number of atom coordinates read : 4447 total number of charged atoms : 4286 net assigned charge : -4.960950 assigned positive charge : 669.3043 centred at (gu) : 90.07771 89.18656 89.54964 assigned negative charge : -674.2682 centred at (gu) : 90.29198 89.14211 89.47282 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7860 nv = 96 ne = 84 npr = 93284 no. pairs analyzed = 93284 no. exposed pairs = 4992 no. arc points = 34423 no. surface atoms = 1688 nbur = 2759 mkacc time = 0.1600000 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 = 1.624000 m= 299 mr = 4515 m= 0 mr = 11 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 76 time to turn everything in is 0.3100000 number of dielectric boundary points 3633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3525 ## 519 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 10588 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.3748334E-10 2.2589124E-10 midg,1,midg; midg,igrid,midg -4.8244631E-10 6.6883915E-11 1,midg,midg; igrid,midg,midg 9.4393970E-10 -1.3590720E-09 gauss-seidel spectral radius is 0.9817272 estimated iterations to convergence 61 setup time was (sec) 0.5700000 now iterating at: 11:45:25 rms-change max change #iterations 7.9413801E-02 14.70389 at 10iterations 5.4722968E-03 0.7656651 at 20iterations 6.9356401E-04 9.4419479E-02 at 30iterations 1.8510286E-04 2.6264429E-02 at 40iterations 5.9388240E-05 8.9931488E-03 at 50iterations finished qdiffx linear iterations at : 11:45:29 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 5.9388240E-05 8.9931488E-03 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 11:45:30 4.571u 0.301s 0:05.23 93.1% 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 Sat Oct 8 2011 at 11:45:30 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4447 !!! WARNING: SEP 283 has a net charge of -0.4750 !!! WARNING: HIT 437 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.588742 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): 59.16500 114.6770 ymin,ymax (A): 19.09800 86.32100 zmin,zma (A): -7.708000 55.57300 x,y,z range (A): 55.51200 67.22300 63.28100 scale (grids/A): 1.588742 object centre (A): 86.92100 52.70950 23.93250 number of atom coordinates read : 4447 total number of charged atoms : 4286 net assigned charge : -4.960950 assigned positive charge : 669.3043 centred at (gu) : 90.23177 87.55843 88.64788 assigned negative charge : -674.2682 centred at (gu) : 90.87552 87.42546 88.41821 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 88968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34423 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 27497 mr = 64060 m= 2646 mr = 19532 m= 46 mr = 1429 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 5791 time to turn everything in is 0.4600000 number of dielectric boundary points 34134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 457 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 32617 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) : 0.5295807 object centre at (A) : 86.92100 52.70950 23.93250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0641489E-02 8.3689194E-04 midg,1,midg; midg,igrid,midg -2.3651810E-02 1.2386562E-02 1,midg,midg; igrid,midg,midg 2.0814911E-02 -2.2596551E-02 gauss-seidel spectral radius is 0.9982147 estimated iterations to convergence 188 setup time was (sec) 0.7700000 now iterating at: 11:45:31 rms-change max change #iterations 3.981670 149.3575 at 10iterations 1.672884 52.88705 at 20iterations 0.7037390 23.11218 at 30iterations 0.2956955 9.484436 at 40iterations 0.1247207 4.281239 at 50iterations 5.2729513E-02 1.822459 at 60iterations 2.2243455E-02 0.7189426 at 70iterations 9.4342278E-03 0.2834339 at 80iterations 4.0332018E-03 0.1249862 at 90iterations 1.7626098E-03 5.9334278E-02 at 100iterations 8.0405775E-04 2.7462006E-02 at 110iterations 3.9494064E-04 1.3119698E-02 at 120iterations finished qdiffx linear iterations at : 11:45:40 total time elapsed so far: 9.860000 # loops : 120 mean,max change (kT/e) : 3.9494064E-04 1.3119698E-02 energy calculations done at 9.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.00000 DelPhi exited at 11:45:41 10.001u 0.340s 0:10.93 94.6% 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 11:45:41 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4447 !!! WARNING: SEP 283 has a net charge of -0.4750 !!! WARNING: HIT 437 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.383113 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): 59.16500 114.6770 ymin,ymax (A): 19.09800 86.32100 zmin,zma (A): -7.708000 55.57300 x,y,z range (A): 55.51200 67.22300 63.28100 scale (grids/A): 2.383113 object centre (A): 86.92100 52.70950 23.93250 number of atom coordinates read : 4447 total number of charged atoms : 4286 net assigned charge : -4.960950 assigned positive charge : 669.3043 centred at (gu) : 90.34727 86.33733 87.97143 assigned negative charge : -674.2682 centred at (gu) : 91.31322 86.13808 87.62720 start vw surface at 0.1100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 207268 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34423 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 97043 mr = 155745 m= 26578 mr = 79109 m= 4113 mr = 20482 m= 233 mr = 2871 m= 4 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 19847 time to turn everything in is 1.090000 number of dielectric boundary points 76942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 34236 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) : 1.588742 object centre at (A) : 86.92100 52.70950 23.93250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3468261 6.2774912E-02 midg,1,midg; midg,igrid,midg -0.8107741 0.1486250 1,midg,midg; igrid,midg,midg 0.3539738 -0.3316500 gauss-seidel spectral radius is 0.9991691 estimated iterations to convergence 274 setup time was (sec) 1.350000 now iterating at: 11:45:42 rms-change max change #iterations 10.37245 392.8123 at 10iterations 5.907170 129.0511 at 20iterations 3.335841 103.2182 at 30iterations 1.880840 40.08763 at 40iterations 1.057795 22.40668 at 50iterations 0.5930687 13.07168 at 60iterations 0.3321169 6.505467 at 70iterations 0.1855693 3.571396 at 80iterations 0.1038384 1.895058 at 90iterations 5.7779919E-02 1.219524 at 100iterations 3.2277826E-02 0.6061745 at 110iterations 1.8027488E-02 0.3096976 at 120iterations 1.0047060E-02 0.1735229 at 130iterations 5.6324187E-03 0.1058502 at 140iterations 3.1743045E-03 5.7813644E-02 at 150iterations 1.8037714E-03 3.2092094E-02 at 160iterations 1.0428578E-03 1.8522739E-02 at 170iterations 6.2118622E-04 1.1352539E-02 at 180iterations finished qdiffx linear iterations at : 11:45:55 total time elapsed so far: 14.04000 # loops : 180 mean,max change (kT/e) : 6.2118622E-04 1.1352539E-02 energy calculations done at 14.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.18000 DelPhi exited at 11:45:56 14.181u 0.272s 0:14.81 97.5% 0+0k 0+0io 0pf+0w