Tue Oct 11 08:16:40 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 Tue Oct 11 2011 at 08:16:40 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 !!! WARNING: GLM 10 has a net charge of -0.0940 !!! WARNING: HIR 19 has a net charge of 0.5140 !!! WARNING: FMN 701 has a net charge of -2.0000 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: 0.3191995 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): 55.41700 132.2470 ymin,ymax (A): 31.86200 104.3140 zmin,zma (A): 46.89200 158.4210 x,y,z range (A): 76.82999 72.45200 111.5290 scale (grids/A): 0.3191995 object centre (A): 93.83200 68.08801 102.6565 number of atom coordinates read : 2622 total number of charged atoms : 2454 net assigned charge : 2.420013 assigned positive charge : 397.7598 centred at (gu) : 85.59925 86.56269 98.89333 assigned negative charge : -395.3406 centred at (gu) : 85.73288 86.70866 98.77126 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 1395 nv = 96 ne = 84 npr = 53832 no. pairs analyzed = 53832 no. exposed pairs = 3257 no. arc points = 22933 no. surface atoms = 1094 nbur = 1528 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.708160 m= 17 mr = 576 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1289 ## 457 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 2059 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.5242444E-18 1.2208553E-14 midg,1,midg; midg,igrid,midg 1.3144244E-15 -9.3112955E-17 1,midg,midg; igrid,midg,midg 1.8135291E-15 -5.8395351E-17 gauss-seidel spectral radius is 0.9506273 estimated iterations to convergence 38 setup time was (sec) 0.3900000 now iterating at: 08:16:41 rms-change max change #iterations 3.6971171E-03 1.275480 at 10iterations 3.4817549E-05 1.4560699E-02 at 20iterations 4.3093968E-07 1.2207031E-04 at 30iterations 1.8966764E-08 7.6293945E-06 at 40iterations 1.9421257E-08 7.6293945E-06 at 50iterations finished qdiffx linear iterations at : 08:16:45 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 1.9421257E-08 7.6293945E-06 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 08:16:45 4.401u 0.176s 0:04.95 92.3% 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 Tue Oct 11 2011 at 08:16:45 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 !!! WARNING: GLM 10 has a net charge of -0.0940 !!! WARNING: HIR 19 has a net charge of 0.5140 !!! WARNING: FMN 701 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.9575984 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): 55.41700 132.2470 ymin,ymax (A): 31.86200 104.3140 zmin,zma (A): 46.89200 158.4210 x,y,z range (A): 76.82999 72.45200 111.5290 scale (grids/A): 0.9575984 object centre (A): 93.83200 68.08801 102.6565 number of atom coordinates read : 2622 total number of charged atoms : 2454 net assigned charge : 2.420013 assigned positive charge : 397.7598 centred at (gu) : 76.79716 79.68735 116.6793 assigned negative charge : -395.3406 centred at (gu) : 77.19836 80.12567 116.3137 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 17708 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22933 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.436000 m= 2237 mr = 10873 m= 42 mr = 937 m= 0 mr = 0 time to grow re-entrant surface = 4.0000007E-02 no. cavity mid-points inaccessible to solvent = 124 time to turn everything in is 0.1500000 number of dielectric boundary points 8177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 851 ## 63 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 13824 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) : 0.3191995 object centre at (A) : 93.83200 68.08801 102.6565 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4120955E-05 8.5983134E-05 midg,1,midg; midg,igrid,midg 7.7413635E-05 -9.4375764E-06 1,midg,midg; igrid,midg,midg 4.6683523E-05 -8.2282395E-06 gauss-seidel spectral radius is 0.9942842 estimated iterations to convergence 107 setup time was (sec) 0.3500000 now iterating at: 08:16:46 rms-change max change #iterations 0.7250011 82.10636 at 10iterations 0.1517337 13.23491 at 20iterations 3.2629650E-02 2.797579 at 30iterations 6.9019082E-03 0.5667966 at 40iterations 1.4763612E-03 0.1262169 at 50iterations 3.1256388E-04 2.5558472E-02 at 60iterations 6.7498841E-05 5.2642822E-03 at 70iterations 1.4379434E-05 1.2154579E-03 at 80iterations 3.0778097E-06 2.5177002E-04 at 90iterations 7.1412342E-07 6.1035156E-05 at 100iterations 2.9829371E-07 3.0517578E-05 at 110iterations 2.5457280E-07 3.0517578E-05 at 120iterations finished qdiffx linear iterations at : 08:16:52 total time elapsed so far: 7.030000 # loops : 120 mean,max change (kT/e) : 2.5457280E-07 3.0517578E-05 energy calculations done at 7.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.170000 DelPhi exited at 08:16:53 7.171u 0.196s 0:07.70 95.5% 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 Tue Oct 11 2011 at 08:16:53 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 !!! WARNING: GLM 10 has a net charge of -0.0940 !!! WARNING: HIR 19 has a net charge of 0.5140 !!! WARNING: FMN 701 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.436398 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): 55.41700 132.2470 ymin,ymax (A): 31.86200 104.3140 zmin,zma (A): 46.89200 158.4210 x,y,z range (A): 76.82999 72.45200 111.5290 scale (grids/A): 1.436398 object centre (A): 93.83200 68.08801 102.6565 number of atom coordinates read : 2622 total number of charged atoms : 2454 net assigned charge : 2.420013 assigned positive charge : 397.7598 centred at (gu) : 70.19553 74.53085 130.0188 assigned negative charge : -395.3406 centred at (gu) : 70.79756 75.18839 129.4706 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 42317 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22933 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.408000 m= 10787 mr = 28073 m= 670 mr = 6932 m= 10 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 424 time to turn everything in is 0.2700000 number of dielectric boundary points 18601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 348 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 17973 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) : 0.9575984 object centre at (A) : 93.83200 68.08801 102.6565 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8790647E-04 -5.0910249E-02 midg,1,midg; midg,igrid,midg 3.4822600E-03 -1.9060947E-04 1,midg,midg; igrid,midg,midg -1.3696384E-03 -1.4273894E-04 gauss-seidel spectral radius is 0.9973792 estimated iterations to convergence 156 setup time was (sec) 0.4900000 now iterating at: 08:16:54 rms-change max change #iterations 2.723825 203.0470 at 10iterations 0.9947264 52.81244 at 20iterations 0.3560654 18.54138 at 30iterations 0.1266880 6.515844 at 40iterations 4.4833019E-02 2.268944 at 50iterations 1.5865812E-02 0.6984177 at 60iterations 5.5928277E-03 0.2423248 at 70iterations 1.9721866E-03 9.2113495E-02 at 80iterations 6.9497392E-04 2.9209137E-02 at 90iterations 2.4476091E-04 1.1054993E-02 at 100iterations 8.5905325E-05 3.5705566E-03 at 110iterations 3.0364499E-05 1.4190674E-03 at 120iterations 1.0690660E-05 4.7022104E-04 at 130iterations 3.8090075E-06 1.6784668E-04 at 140iterations 1.4669208E-06 6.1035156E-05 at 150iterations 7.6962783E-07 6.1035156E-05 at 160iterations 6.2665373E-07 6.1035156E-05 at 170iterations 6.1020205E-07 6.1035156E-05 at 180iterations finished qdiffx linear iterations at : 08:17:04 total time elapsed so far: 10.63000 # loops : 180 mean,max change (kT/e) : 6.1020205E-07 6.1035156E-05 energy calculations done at 10.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.76000 DelPhi exited at 08:17:04 10.761u 0.206s 0:11.37 96.3% 0+0k 0+0io 0pf+0w