Sat Oct 8 19:52:26 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 19:52:26 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 88.45930 89.12758 89.59661 assigned negative charge : -387.9385 centred at (gu) : 88.36340 89.17386 89.48683 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 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 0.3100000 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 0.4500000 number of grid points assigned charge 8015 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4718567E-09 9.4618864E-09 midg,1,midg; midg,igrid,midg 7.5685058E-09 1.6846838E-10 1,midg,midg; igrid,midg,midg -4.5313717E-09 6.7487460E-09 gauss-seidel spectral radius is 0.9865081 estimated iterations to convergence 70 setup time was (sec) 0.6200000 now iterating at: 19:52:27 rms-change max change #iterations 0.1263239 18.57420 at 10iterations 1.1611968E-02 1.775715 at 20iterations 1.0859335E-03 0.1598969 at 30iterations 9.9976540E-05 1.3799667E-02 at 40iterations 9.0773538E-06 1.3484955E-03 at 50iterations finished qdiffx linear iterations at : 19:52:30 total time elapsed so far: 4.150000 # loops : 50 mean,max change (kT/e) : 9.0773538E-06 1.3484955E-03 energy calculations done at 4.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 19:52:31 4.348u 0.289s 0:04.91 94.0% 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 19:52:31 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 85.37711 87.38232 88.78928 assigned negative charge : -387.9385 centred at (gu) : 85.09003 87.52130 88.46029 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 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 0.6600000 number of grid points assigned charge 19220 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 -1.6240347E-02 2.4400601E-02 midg,1,midg; midg,igrid,midg 1.1592803E-02 2.5235722E-03 1,midg,midg; igrid,midg,midg -3.5073112E-03 3.3997089E-02 gauss-seidel spectral radius is 0.9985615 estimated iterations to convergence 209 setup time was (sec) 0.8700000 now iterating at: 19:52:32 rms-change max change #iterations 4.042063 155.3294 at 10iterations 1.853387 66.38056 at 20iterations 0.8496693 29.36845 at 30iterations 0.3904705 12.42561 at 40iterations 0.1792611 6.290363 at 50iterations 8.2268491E-02 2.534267 at 60iterations 3.7878931E-02 1.309063 at 70iterations 1.7396621E-02 0.6458660 at 80iterations 7.9780705E-03 0.2654308 at 90iterations 3.6551759E-03 0.1230087 at 100iterations 1.6889162E-03 6.9608688E-02 at 110iterations 7.7350723E-04 2.6430607E-02 at 120iterations finished qdiffx linear iterations at : 19:52:41 total time elapsed so far: 9.740000 # loops : 120 mean,max change (kT/e) : 7.7350723E-04 2.6430607E-02 energy calculations done at 9.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.960000 DelPhi exited at 19:52:42 9.958u 0.334s 0:10.62 96.7% 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 19:52:42 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 83.06564 86.07341 88.18386 assigned negative charge : -387.9385 centred at (gu) : 82.63504 86.28185 87.69032 start vw surface at 0.1900000 fill in re-entrant regions at 0.5700000 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 = 0.7499999 no. cavity mid-points inaccessible to solvent = 16815 time to turn everything in is 1.450000 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 1.600000 number of grid points assigned charge 19598 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 -9.4275281E-02 0.3240660 midg,1,midg; midg,igrid,midg 0.1404581 3.3032816E-02 1,midg,midg; igrid,midg,midg -3.4337804E-02 0.4150186 gauss-seidel spectral radius is 0.9992310 estimated iterations to convergence 285 setup time was (sec) 1.860000 now iterating at: 19:52:44 rms-change max change #iterations 9.429006 542.8687 at 10iterations 5.404076 122.5696 at 20iterations 3.076914 64.03052 at 30iterations 1.750537 39.60157 at 40iterations 0.9949526 17.95177 at 50iterations 0.5655914 11.79055 at 60iterations 0.3216198 6.126210 at 70iterations 0.1821103 3.547115 at 80iterations 0.1036905 2.013618 at 90iterations 5.8876604E-02 1.207195 at 100iterations 3.3400521E-02 0.6317401 at 110iterations 1.8994635E-02 0.3555756 at 120iterations 1.0772857E-02 0.2083340 at 130iterations 6.1102491E-03 0.1064434 at 140iterations 3.4647251E-03 6.2866211E-02 at 150iterations 1.9685118E-03 3.8754463E-02 at 160iterations 1.1215883E-03 1.9599915E-02 at 170iterations 6.3591724E-04 1.3108253E-02 at 180iterations finished qdiffx linear iterations at : 19:52:58 total time elapsed so far: 16.03000 # loops : 180 mean,max change (kT/e) : 6.3591724E-04 1.3108253E-02 energy calculations done at 16.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.21000 DelPhi exited at 19:52:58 16.208u 0.307s 0:16.78 98.3% 0+0k 0+0io 0pf+0w