Sat Oct 15 14:08:10 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 15 2011 at 14:08:10 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4731 !!! WARNING: HEM 819 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5092335 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): -16.14700 36.80000 ymin,ymax (A): -31.02900 35.61200 zmin,zma (A): -4.174000 65.73500 x,y,z range (A): 52.94700 66.64101 69.90900 scale (grids/A): 0.5092335 object centre (A): 10.32650 2.291502 30.78050 number of atom coordinates read : 4731 total number of charged atoms : 4485 net assigned charge : 5.800022 assigned positive charge : 707.4486 centred at (gu) : 89.69135 90.57559 88.16771 assigned negative charge : -701.6530 centred at (gu) : 89.59682 90.62218 88.16056 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7905 nv = 96 ne = 84 npr = 94234 no. pairs analyzed = 94234 no. exposed pairs = 6037 no. arc points = 41826 no. surface atoms = 2027 nbur = 2704 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 = 1.680000 m= 284 mr = 4118 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3992 ## 577 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 10411 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9058831E-11 6.0117959E-11 midg,1,midg; midg,igrid,midg 1.6316834E-10 -3.9271694E-11 1,midg,midg; igrid,midg,midg -1.6328679E-10 2.7861477E-10 gauss-seidel spectral radius is 0.9802814 estimated iterations to convergence 59 setup time was (sec) 0.5800000 now iterating at: 14:08:12 rms-change max change #iterations 6.8011269E-02 9.865570 at 10iterations 3.8243569E-03 0.5593338 at 20iterations 3.1350492E-04 4.9522400E-02 at 30iterations 7.7388046E-05 9.6041560E-03 at 40iterations 2.9443954E-05 4.3268204E-03 at 50iterations finished qdiffx linear iterations at : 14:08:18 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 2.9443954E-05 4.3268204E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 14:08:19 3.993u 0.212s 0:09.08 46.2% 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 Sat Oct 15 2011 at 14:08:20 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4731 !!! WARNING: HEM 819 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.527700 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): -16.14700 36.80000 ymin,ymax (A): -31.02900 35.61200 zmin,zma (A): -4.174000 65.73500 x,y,z range (A): 52.94700 66.64101 69.90900 scale (grids/A): 1.527700 object centre (A): 10.32650 2.291502 30.78050 number of atom coordinates read : 4731 total number of charged atoms : 4485 net assigned charge : 5.800022 assigned positive charge : 707.4486 centred at (gu) : 89.07272 91.72517 84.50194 assigned negative charge : -701.6530 centred at (gu) : 88.79012 91.86635 84.48129 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 89778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41826 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25921 mr = 61805 m= 2225 mr = 17152 m= 38 mr = 957 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 102 time to turn everything in is 0.4500000 number of dielectric boundary points 38049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 522 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 33695 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) : 0.5092335 object centre at (A) : 10.32650 2.291502 30.78050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9359975E-03 1.5649909E-02 midg,1,midg; midg,igrid,midg 3.4704602E-03 -1.2330763E-02 1,midg,midg; igrid,midg,midg -4.5601459E-04 1.0484949E-02 gauss-seidel spectral radius is 0.9981036 estimated iterations to convergence 182 setup time was (sec) 0.7200000 now iterating at: 14:08:22 rms-change max change #iterations 3.734167 148.8103 at 10iterations 1.516739 56.86606 at 20iterations 0.6229115 20.44111 at 30iterations 0.2550271 7.755779 at 40iterations 0.1040152 3.401270 at 50iterations 4.2806886E-02 1.372053 at 60iterations 1.7513435E-02 0.5886917 at 70iterations 7.1808849E-03 0.2573204 at 80iterations 2.9524060E-03 9.5827103E-02 at 90iterations 1.2165260E-03 3.9590836E-02 at 100iterations 5.0324906E-04 1.5753984E-02 at 110iterations 2.1160216E-04 6.9532394E-03 at 120iterations finished qdiffx linear iterations at : 14:08:35 total time elapsed so far: 8.880000 # loops : 120 mean,max change (kT/e) : 2.1160216E-04 6.9532394E-03 energy calculations done at 8.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.000000 DelPhi exited at 14:08:36 9.004u 0.283s 0:16.20 57.2% 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 Sat Oct 15 2011 at 14:08:38 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4731 !!! WARNING: HEM 819 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.291551 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): -16.14700 36.80000 ymin,ymax (A): -31.02900 35.61200 zmin,zma (A): -4.174000 65.73500 x,y,z range (A): 52.94700 66.64101 69.90900 scale (grids/A): 2.291551 object centre (A): 10.32650 2.291502 30.78050 number of atom coordinates read : 4731 total number of charged atoms : 4485 net assigned charge : 5.800022 assigned positive charge : 707.4486 centred at (gu) : 88.60860 92.58763 81.75258 assigned negative charge : -701.6530 centred at (gu) : 88.18520 92.79955 81.72193 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 209518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41826 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93267 mr = 151902 m= 22930 mr = 72957 m= 3142 mr = 16362 m= 162 mr = 1931 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 373 time to turn everything in is 1.130000 number of dielectric boundary points 85818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 35778 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) : 1.527700 object centre at (A) : 10.32650 2.291502 30.78050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1384897 0.4120766 midg,1,midg; midg,igrid,midg -3.0496327E-02 -0.2932562 1,midg,midg; igrid,midg,midg -8.0357073E-03 0.1661604 gauss-seidel spectral radius is 0.9991593 estimated iterations to convergence 272 setup time was (sec) 1.470000 now iterating at: 14:08:40 rms-change max change #iterations 10.08062 260.8988 at 10iterations 5.770187 133.7293 at 20iterations 3.271332 84.58170 at 30iterations 1.844216 41.14641 at 40iterations 1.036969 24.42425 at 50iterations 0.5810999 12.69473 at 60iterations 0.3253780 7.578109 at 70iterations 0.1817471 3.543726 at 80iterations 0.1013846 2.022297 at 90iterations 5.6401793E-02 1.390705 at 100iterations 3.1393420E-02 0.6600342 at 110iterations 1.7448973E-02 0.3135452 at 120iterations 9.6808039E-03 0.2086163 at 130iterations 5.3901379E-03 9.6385956E-02 at 140iterations 2.9907252E-03 5.4351807E-02 at 150iterations 1.6614926E-03 3.0396461E-02 at 160iterations 9.2139846E-04 1.9268036E-02 at 170iterations 5.1119621E-04 9.2453957E-03 at 180iterations finished qdiffx linear iterations at : 14:09:03 total time elapsed so far: 14.72000 # loops : 180 mean,max change (kT/e) : 5.1119621E-04 9.2453957E-03 energy calculations done at 14.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.85000 DelPhi exited at 14:09:04 14.855u 0.365s 0:26.00 58.5% 0+0k 0+0io 0pf+0w