Mon Oct 10 09:18:04 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 09:18:04 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2873 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5623479 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): 109.5920 172.8980 ymin,ymax (A): -44.61100 7.578000 zmin,zma (A): 49.44600 104.7160 x,y,z range (A): 63.30600 52.18900 55.27000 scale (grids/A): 0.5623479 object centre (A): 141.2450 -18.51650 77.08099 number of atom coordinates read : 2873 total number of charged atoms : 2721 net assigned charge : 7.014014 assigned positive charge : 423.7628 centred at (gu) : 90.80776 88.36129 88.59115 assigned negative charge : -416.7494 centred at (gu) : 90.84154 88.45953 88.41865 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6220 nv = 96 ne = 84 npr = 55154 no. pairs analyzed = 55154 no. exposed pairs = 4299 no. arc points = 31392 no. surface atoms = 1437 nbur = 1436 mkacc time = 8.9999996E-02 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 = 1.512000 m= 312 mr = 2759 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3132 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7868 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6503993E-09 1.9405895E-09 midg,1,midg; midg,igrid,midg 2.8474854E-09 -1.8414874E-10 1,midg,midg; igrid,midg,midg 9.9358444E-10 5.3338783E-10 gauss-seidel spectral radius is 0.9836996 estimated iterations to convergence 64 setup time was (sec) 0.4100000 now iterating at: 09:18:04 rms-change max change #iterations 8.7712049E-02 22.67421 at 10iterations 6.1718286E-03 1.148804 at 20iterations 4.3860107E-04 9.3177795E-02 at 30iterations 3.3821882E-05 5.4206848E-03 at 40iterations 3.5161320E-06 5.1116943E-04 at 50iterations finished qdiffx linear iterations at : 09:18:07 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.5161320E-06 5.1116943E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 09:18:08 3.430u 0.178s 0:04.03 89.3% 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 Mon Oct 10 2011 at 09:18:08 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2873 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 1.687044 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): 109.5920 172.8980 ymin,ymax (A): -44.61100 7.578000 zmin,zma (A): 49.44600 104.7160 x,y,z range (A): 63.30600 52.18900 55.27000 scale (grids/A): 1.687044 object centre (A): 141.2450 -18.51650 77.08099 number of atom coordinates read : 2873 total number of charged atoms : 2721 net assigned charge : 7.014014 assigned positive charge : 423.7628 centred at (gu) : 92.42290 85.08315 85.77319 assigned negative charge : -416.7494 centred at (gu) : 92.52422 85.37824 85.25569 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31392 grid for indexing accessible points = 1.400000 m= 21864 mr = 40013 m= 3074 mr = 14321 m= 115 mr = 1541 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 34984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20999 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) : 0.5623479 object centre at (A) : 141.2450 -18.51650 77.08099 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2876870E-03 2.2088919E-02 midg,1,midg; midg,igrid,midg 1.1569815E-02 1.8600288E-03 1,midg,midg; igrid,midg,midg 1.5503156E-02 -4.2947996E-03 gauss-seidel spectral radius is 0.9983197 estimated iterations to convergence 194 setup time was (sec) 0.5800000 now iterating at: 09:18:09 rms-change max change #iterations 3.490826 160.5161 at 10iterations 1.495167 57.84591 at 20iterations 0.6418482 26.91043 at 30iterations 0.2759455 9.476659 at 40iterations 0.1184079 4.363098 at 50iterations 5.0902300E-02 1.816236 at 60iterations 2.1898920E-02 0.8006903 at 70iterations 9.3924617E-03 0.3514938 at 80iterations 4.0507433E-03 0.1508446 at 90iterations 1.7426155E-03 6.2177658E-02 at 100iterations 7.5112883E-04 3.1626701E-02 at 110iterations 3.2210411E-04 1.1936188E-02 at 120iterations finished qdiffx linear iterations at : 09:18:16 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 3.2210411E-04 1.1936188E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 09:18:16 7.826u 0.180s 0:08.28 96.6% 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 09:18:16 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2873 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.530566 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): 109.5920 172.8980 ymin,ymax (A): -44.61100 7.578000 zmin,zma (A): 49.44600 104.7160 x,y,z range (A): 63.30600 52.18900 55.27000 scale (grids/A): 2.530566 object centre (A): 141.2450 -18.51650 77.08099 number of atom coordinates read : 2873 total number of charged atoms : 2721 net assigned charge : 7.014014 assigned positive charge : 423.7628 centred at (gu) : 93.63425 82.62467 83.65952 assigned negative charge : -416.7494 centred at (gu) : 93.78633 83.06727 82.88354 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 151856 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31392 grid for indexing accessible points = 1.400000 m= 70098 mr = 98746 m= 24507 mr = 52811 m= 5262 mr = 18118 m= 465 mr = 3437 m= 9 mr = 172 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8300000 number of dielectric boundary points 78913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 21751 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) : 1.687044 object centre at (A) : 141.2450 -18.51650 77.08099 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1236859 0.3037157 midg,1,midg; midg,igrid,midg 0.1124009 5.4376997E-02 1,midg,midg; igrid,midg,midg 0.1625025 -0.1749098 gauss-seidel spectral radius is 0.9991969 estimated iterations to convergence 279 setup time was (sec) 1.070000 now iterating at: 09:18:17 rms-change max change #iterations 8.971976 341.7163 at 10iterations 5.194845 162.2933 at 20iterations 2.983258 84.24728 at 30iterations 1.700216 42.23083 at 40iterations 0.9641783 23.83491 at 50iterations 0.5466968 13.14171 at 60iterations 0.3089644 7.705410 at 70iterations 0.1746379 4.166583 at 80iterations 9.8317653E-02 2.315279 at 90iterations 5.5264335E-02 1.257801 at 100iterations 3.1092374E-02 0.6512701 at 110iterations 1.7486468E-02 0.4046106 at 120iterations 9.8190838E-03 0.2124048 at 130iterations 5.5082971E-03 0.1211805 at 140iterations 3.0820202E-03 7.2113037E-02 at 150iterations 1.7329088E-03 3.9899588E-02 at 160iterations 9.7106962E-04 1.9958496E-02 at 170iterations 5.4536073E-04 1.1344910E-02 at 180iterations finished qdiffx linear iterations at : 09:18:29 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 5.4536073E-04 1.1344910E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 09:18:29 12.548u 0.218s 0:13.03 97.8% 0+0k 0+0io 0pf+0w