Sat Oct 8 19:51:53 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 8 2011 at 19:51:53 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 622 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6197016 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): -31.34800 17.44600 ymin,ymax (A): -23.68800 23.13400 zmin,zma (A): -12.35700 45.09000 x,y,z range (A): 48.79400 46.82200 57.44700 scale (grids/A): 0.6197016 object centre (A): -6.951000 -0.2770004 16.36650 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.44927 89.13129 89.58866 assigned negative charge : -387.4045 centred at (gu) : 88.35045 89.17788 89.47922 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6332 nv = 96 ne = 84 npr = 54918 no. pairs analyzed = 54918 no. exposed pairs = 2976 no. arc points = 21354 no. surface atoms = 1003 nbur = 1586 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 3480 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.2900000 number of dielectric boundary points 3115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2177 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8021 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3576605E-09 9.4889021E-09 midg,1,midg; midg,igrid,midg 7.6764666E-09 2.2118443E-10 1,midg,midg; igrid,midg,midg -4.6968114E-09 6.9175141E-09 gauss-seidel spectral radius is 0.9865081 estimated iterations to convergence 70 setup time was (sec) 0.5800000 now iterating at: 19:51:54 rms-change max change #iterations 0.1248721 18.12856 at 10iterations 1.1466860E-02 1.749947 at 20iterations 1.0739311E-03 0.1609600 at 30iterations 9.9024350E-05 1.3082504E-02 at 40iterations 8.9895375E-06 1.3332367E-03 at 50iterations finished qdiffx linear iterations at : 19:51:58 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 8.9895375E-06 1.3332367E-03 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 19:51:58 4.344u 0.297s 0:04.90 94.4% 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 Sat Oct 8 2011 at 19:51:58 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 622 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.859105 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): -31.34800 17.44600 ymin,ymax (A): -23.68800 23.13400 zmin,zma (A): -12.35700 45.09000 x,y,z range (A): 48.79400 46.82200 57.44700 scale (grids/A): 1.859105 object centre (A): -6.951000 -0.2770004 16.36650 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.34706 87.39345 88.76536 assigned negative charge : -387.4045 centred at (gu) : 85.05123 87.53335 88.43741 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21354 grid for indexing accessible points = 1.400000 m= 23313 mr = 48227 m= 3193 mr = 17130 m= 155 mr = 1955 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 4888 time to turn everything in is 0.5300000 number of dielectric boundary points 28740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19250 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) : 0.6197016 object centre at (A) : -6.951000 -0.2770004 16.36650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6132906E-02 2.4322301E-02 midg,1,midg; midg,igrid,midg 1.1731447E-02 2.5887324E-03 1,midg,midg; igrid,midg,midg -3.5721024E-03 3.4545194E-02 gauss-seidel spectral radius is 0.9985615 estimated iterations to convergence 209 setup time was (sec) 0.8800000 now iterating at: 19:52:00 rms-change max change #iterations 4.030425 155.3294 at 10iterations 1.847038 67.33199 at 20iterations 0.8467550 29.14822 at 30iterations 0.3892512 12.63244 at 40iterations 0.1786890 6.247334 at 50iterations 8.2023375E-02 2.599354 at 60iterations 3.7757356E-02 1.277161 at 70iterations 1.7336858E-02 0.6330309 at 80iterations 7.9503357E-03 0.2722600 at 90iterations 3.6423095E-03 0.1191483 at 100iterations 1.6833585E-03 6.8119049E-02 at 110iterations 7.7086338E-04 2.6358604E-02 at 120iterations finished qdiffx linear iterations at : 19:52:08 total time elapsed so far: 9.760000 # loops : 120 mean,max change (kT/e) : 7.7086338E-04 2.6358604E-02 energy calculations done at 9.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.950000 DelPhi exited at 19:52:09 9.949u 0.324s 0:10.55 97.2% 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 8 2011 at 19:52:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 622 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.788657 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): -31.34800 17.44600 ymin,ymax (A): -23.68800 23.13400 zmin,zma (A): -12.35700 45.09000 x,y,z range (A): 48.79400 46.82200 57.44700 scale (grids/A): 2.788657 object centre (A): -6.951000 -0.2770004 16.36650 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.02055 86.09009 88.14798 assigned negative charge : -387.4045 centred at (gu) : 82.57684 86.29990 87.65600 start vw surface at 0.1800000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 160965 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21354 grid for indexing accessible points = 1.400000 m= 78009 mr = 117024 m= 25786 mr = 63859 m= 5648 mr = 20650 m= 703 mr = 4191 m= 32 mr = 473 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 16815 time to turn everything in is 1.500000 number of dielectric boundary points 64939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 19630 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) : 1.859105 object centre at (A) : -6.951000 -0.2770004 16.36650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3272135E-02 0.3227956 midg,1,midg; midg,igrid,midg 0.1417292 3.3806883E-02 1,midg,midg; igrid,midg,midg -3.5148643E-02 0.4213063 gauss-seidel spectral radius is 0.9992310 estimated iterations to convergence 285 setup time was (sec) 1.860000 now iterating at: 19:52:11 rms-change max change #iterations 9.402483 542.8688 at 10iterations 5.389402 122.5683 at 20iterations 3.068770 64.03114 at 30iterations 1.745753 39.60894 at 40iterations 0.9922213 17.92052 at 50iterations 0.5641654 11.70100 at 60iterations 0.3208152 6.312329 at 70iterations 0.1816797 3.624283 at 80iterations 0.1034394 2.033119 at 90iterations 5.8724105E-02 1.219458 at 100iterations 3.3314049E-02 0.6307530 at 110iterations 1.8944275E-02 0.3519983 at 120iterations 1.0747123E-02 0.2061882 at 130iterations 6.0951635E-03 0.1062529 at 140iterations 3.4557751E-03 6.2606812E-02 at 150iterations 1.9637975E-03 3.8168907E-02 at 160iterations 1.1188840E-03 2.0275116E-02 at 170iterations 6.3432055E-04 1.3520241E-02 at 180iterations finished qdiffx linear iterations at : 19:52:25 total time elapsed so far: 15.98000 # loops : 180 mean,max change (kT/e) : 6.3432055E-04 1.3520241E-02 energy calculations done at 15.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.16000 DelPhi exited at 19:52:26 16.166u 0.352s 0:16.77 98.4% 0+0k 0+0io 0pf+0w