Mon Oct 10 17:11:49 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 17:11:49 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4626 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5086877 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): -15.94100 37.37100 ymin,ymax (A): -30.78600 34.49400 zmin,zma (A): -4.123000 65.86100 x,y,z range (A): 53.31200 65.28000 69.98400 scale (grids/A): 0.5086877 object centre (A): 10.71500 1.854002 30.86900 number of atom coordinates read : 4626 total number of charged atoms : 4377 net assigned charge : 6.706036 assigned positive charge : 692.4756 centred at (gu) : 89.44785 90.53328 88.05251 assigned negative charge : -685.7740 centred at (gu) : 89.36841 90.60028 88.03285 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7657 nv = 96 ne = 84 npr = 93004 no. pairs analyzed = 93004 no. exposed pairs = 5952 no. arc points = 41563 no. surface atoms = 1990 nbur = 2636 mkacc time = 0.2000000 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= 272 mr = 3952 m= 0 mr = 10 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3984 ## 631 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 10126 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3045882E-11 8.1529179E-11 midg,1,midg; midg,igrid,midg 2.0985363E-10 -7.4809992E-11 1,midg,midg; igrid,midg,midg -1.0879501E-10 2.3281467E-10 gauss-seidel spectral radius is 0.9802294 estimated iterations to convergence 59 setup time was (sec) 0.6800000 now iterating at: 17:11:50 rms-change max change #iterations 6.5648623E-02 9.148724 at 10iterations 3.8139084E-03 0.5741472 at 20iterations 4.7433822E-04 6.5216064E-02 at 30iterations 1.7320905E-04 2.5981188E-02 at 40iterations 7.1555805E-05 1.0791063E-02 at 50iterations finished qdiffx linear iterations at : 17:11:52 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 7.1555805E-05 1.0791063E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 17:11:53 3.525u 0.189s 0:04.16 88.9% 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 Mon Oct 10 2011 at 17:11:53 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4626 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.526063 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): -15.94100 37.37100 ymin,ymax (A): -30.78600 34.49400 zmin,zma (A): -4.123000 65.86100 x,y,z range (A): 53.31200 65.28000 69.98400 scale (grids/A): 1.526063 object centre (A): 10.71500 1.854002 30.86900 number of atom coordinates read : 4626 total number of charged atoms : 4377 net assigned charge : 6.706036 assigned positive charge : 692.4756 centred at (gu) : 88.34217 91.59889 84.15643 assigned negative charge : -685.7740 centred at (gu) : 88.10493 91.80070 84.09850 start vw surface at 0.2300000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 86401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41563 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 24800 mr = 59010 m= 2177 mr = 16362 m= 41 mr = 885 m= 0 mr = 3 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 37159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 562 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 32942 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) : 0.5086877 object centre at (A) : 10.71500 1.854002 30.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3036456E-03 1.8142443E-02 midg,1,midg; midg,igrid,midg 4.1133114E-03 -1.2225289E-02 1,midg,midg; igrid,midg,midg 6.2759512E-04 8.9044413E-03 gauss-seidel spectral radius is 0.9980860 estimated iterations to convergence 182 setup time was (sec) 0.9100000 now iterating at: 17:11:54 rms-change max change #iterations 3.693663 156.2731 at 10iterations 1.500970 57.14296 at 20iterations 0.6146176 19.82883 at 30iterations 0.2503893 8.637427 at 40iterations 0.1019472 3.508644 at 50iterations 4.1723367E-02 1.363379 at 60iterations 1.7062305E-02 0.5435181 at 70iterations 7.0287134E-03 0.2564316 at 80iterations 2.9340861E-03 0.1014805 at 90iterations 1.2622700E-03 4.0189266E-02 at 100iterations 5.9460226E-04 2.0057678E-02 at 110iterations 3.2107689E-04 1.1255264E-02 at 120iterations finished qdiffx linear iterations at : 17:12:00 total time elapsed so far: 7.050000 # loops : 120 mean,max change (kT/e) : 3.2107689E-04 1.1255264E-02 energy calculations done at 7.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 17:12:01 7.223u 0.209s 0:07.94 93.4% 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 17:12:01 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4626 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.289095 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): -15.94100 37.37100 ymin,ymax (A): -30.78600 34.49400 zmin,zma (A): -4.123000 65.86100 x,y,z range (A): 53.31200 65.28000 69.98400 scale (grids/A): 2.289095 object centre (A): 10.71500 1.854002 30.86900 number of atom coordinates read : 4626 total number of charged atoms : 4377 net assigned charge : 6.706036 assigned positive charge : 692.4756 centred at (gu) : 87.51290 92.39784 81.23433 assigned negative charge : -685.7740 centred at (gu) : 87.15741 92.70094 81.14778 start vw surface at 0.1900000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 201272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41563 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 89381 mr = 144926 m= 22216 mr = 69686 m= 3047 mr = 15677 m= 145 mr = 1805 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.400000 number of dielectric boundary points 83917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 34925 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) : 1.526063 object centre at (A) : 10.71500 1.854002 30.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1227939 0.4445678 midg,1,midg; midg,igrid,midg 3.4947459E-02 -0.2799585 1,midg,midg; igrid,midg,midg 2.6082455E-03 0.1395167 gauss-seidel spectral radius is 0.9991522 estimated iterations to convergence 271 setup time was (sec) 1.700000 now iterating at: 17:12:03 rms-change max change #iterations 10.00006 255.9544 at 10iterations 5.705241 129.9915 at 20iterations 3.227889 76.56827 at 30iterations 1.818801 50.51532 at 40iterations 1.021400 22.08272 at 50iterations 0.5719498 12.15750 at 60iterations 0.3191157 6.899109 at 70iterations 0.1775613 3.839931 at 80iterations 9.8727673E-02 2.213881 at 90iterations 5.4956175E-02 1.044880 at 100iterations 3.0501567E-02 0.6056786 at 110iterations 1.6936351E-02 0.3437567 at 120iterations 9.3766935E-03 0.1963215 at 130iterations 5.2065914E-03 9.8592758E-02 at 140iterations 2.8896080E-03 6.2543154E-02 at 150iterations 1.6075951E-03 3.4742355E-02 at 160iterations 8.9723850E-04 1.7196655E-02 at 170iterations 5.0514244E-04 1.0173082E-02 at 180iterations finished qdiffx linear iterations at : 17:12:14 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 5.0514244E-04 1.0173082E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 17:12:14 12.414u 0.232s 0:13.00 97.2% 0+0k 0+0io 0pf+0w