Sat Oct 8 11:41:40 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 11:41:40 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 !!! WARNING: GLM 259 has a net charge of -0.0940 !!! WARNING: HIR 331 has a net charge of 0.5140 !!! WARNING: GLM 355 has a net charge of -0.0940 !!! WARNING: HIR 361 has a net charge of 0.5140 !!! WARNING: HIR 491 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.4869175 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): -53.47900 7.154000 ymin,ymax (A): -56.40500 16.70800 zmin,zma (A): -69.47000 -4.045000 x,y,z range (A): 60.63300 73.11301 65.42500 scale (grids/A): 0.4869175 object centre (A): -23.16250 -19.84850 -36.75750 number of atom coordinates read : 5505 total number of charged atoms : 5328 net assigned charge : -0.6459424 assigned positive charge : 841.7480 centred at (gu) : 89.63670 90.07619 89.86780 assigned negative charge : -842.4002 centred at (gu) : 89.60361 90.10911 89.87903 start vw surface at 0.2700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 7865 nv = 96 ne = 84 npr = 113191 no. pairs analyzed = 113191 no. exposed pairs = 6916 no. arc points = 47119 no. surface atoms = 2326 nbur = 3179 mkacc time = 0.3300000 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 = 1.736000 m= 282 mr = 3998 m= 5 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 4150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4481 ## 775 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 10898 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3294686E-12 -1.4278131E-11 midg,1,midg; midg,igrid,midg 3.1144892E-11 -3.8739290E-11 1,midg,midg; igrid,midg,midg -4.2173643E-11 2.8898512E-11 gauss-seidel spectral radius is 0.9784822 estimated iterations to convergence 56 setup time was (sec) 0.9200000 now iterating at: 11:41:41 rms-change max change #iterations 5.8186118E-02 9.046946 at 10iterations 4.0527205E-03 0.7602272 at 20iterations 8.8215590E-04 0.1483078 at 30iterations 3.4431924E-04 3.5537720E-02 at 40iterations 1.5177870E-04 1.4889002E-02 at 50iterations finished qdiffx linear iterations at : 11:41:44 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 1.5177870E-04 1.4889002E-02 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 11:41:45 4.319u 0.166s 0:04.82 92.7% 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 11:41:45 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 !!! WARNING: GLM 259 has a net charge of -0.0940 !!! WARNING: HIR 331 has a net charge of 0.5140 !!! WARNING: GLM 355 has a net charge of -0.0940 !!! WARNING: HIR 361 has a net charge of 0.5140 !!! WARNING: HIR 491 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.460752 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): -53.47900 7.154000 ymin,ymax (A): -56.40500 16.70800 zmin,zma (A): -69.47000 -4.045000 x,y,z range (A): 60.63300 73.11301 65.42500 scale (grids/A): 1.460752 object centre (A): -23.16250 -19.84850 -36.75750 number of atom coordinates read : 5505 total number of charged atoms : 5328 net assigned charge : -0.6459424 assigned positive charge : 841.7480 centred at (gu) : 88.90834 90.22711 89.60150 assigned negative charge : -842.4002 centred at (gu) : 88.81068 90.32681 89.63676 start vw surface at 0.2800000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 88961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47119 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 25737 mr = 60523 m= 2084 mr = 16833 m= 37 mr = 729 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 970 time to turn everything in is 0.8600000 number of dielectric boundary points 38734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 668 ## 11 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 39290 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) : 0.4869175 object centre at (A) : -23.16250 -19.84850 -36.75750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6597722E-03 -4.5600594E-03 midg,1,midg; midg,igrid,midg 2.0833170E-02 -1.0124488E-03 1,midg,midg; igrid,midg,midg -1.4147972E-03 2.0368139E-03 gauss-seidel spectral radius is 0.9979628 estimated iterations to convergence 176 setup time was (sec) 1.210000 now iterating at: 11:41:46 rms-change max change #iterations 3.706305 152.0897 at 10iterations 1.459641 50.69324 at 20iterations 0.5779052 23.00295 at 30iterations 0.2285138 7.847265 at 40iterations 9.0955704E-02 2.719158 at 50iterations 3.6249582E-02 1.201767 at 60iterations 1.4558428E-02 0.4736519 at 70iterations 5.9715309E-03 0.2161031 at 80iterations 2.5785633E-03 8.5372925E-02 at 90iterations 1.2636620E-03 3.6876678E-02 at 100iterations 7.3303893E-04 1.8670082E-02 at 110iterations 4.9156381E-04 1.1845112E-02 at 120iterations finished qdiffx linear iterations at : 11:41:54 total time elapsed so far: 9.010000 # loops : 120 mean,max change (kT/e) : 4.9156381E-04 1.1845112E-02 energy calculations done at 9.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.240000 DelPhi exited at 11:41:55 9.238u 0.258s 0:09.80 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 11:41:55 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 !!! WARNING: GLM 259 has a net charge of -0.0940 !!! WARNING: HIR 331 has a net charge of 0.5140 !!! WARNING: GLM 355 has a net charge of -0.0940 !!! WARNING: HIR 361 has a net charge of 0.5140 !!! WARNING: HIR 491 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.191128 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): -53.47900 7.154000 ymin,ymax (A): -56.40500 16.70800 zmin,zma (A): -69.47000 -4.045000 x,y,z range (A): 60.63300 73.11301 65.42500 scale (grids/A): 2.191128 object centre (A): -23.16250 -19.84850 -36.75750 number of atom coordinates read : 5505 total number of charged atoms : 5328 net assigned charge : -0.6459424 assigned positive charge : 841.7480 centred at (gu) : 88.36214 90.34019 89.40198 assigned negative charge : -842.4002 centred at (gu) : 88.21591 90.49033 89.45489 start vw surface at 0.2700000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 207541 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47119 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 92079 mr = 149315 m= 22947 mr = 71070 m= 2930 mr = 16112 m= 127 mr = 1588 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 3358 time to turn everything in is 2.010000 number of dielectric boundary points 87514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 42442 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) : 1.460752 object centre at (A) : -23.16250 -19.84850 -36.75750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2808907E-02 -4.0412046E-02 midg,1,midg; midg,igrid,midg 0.6217524 -3.5465494E-02 1,midg,midg; igrid,midg,midg 2.5709644E-03 5.4295313E-02 gauss-seidel spectral radius is 0.9991340 estimated iterations to convergence 268 setup time was (sec) 2.380000 now iterating at: 11:41:57 rms-change max change #iterations 10.49895 269.6505 at 10iterations 5.997873 141.5748 at 20iterations 3.403307 81.55727 at 30iterations 1.921130 44.95939 at 40iterations 1.084036 23.90380 at 50iterations 0.6074291 11.79412 at 60iterations 0.3393510 7.107936 at 70iterations 0.1893777 3.839796 at 80iterations 0.1052630 2.287799 at 90iterations 5.8665384E-02 1.118408 at 100iterations 3.2509226E-02 0.6987991 at 110iterations 1.8055417E-02 0.3753366 at 120iterations 1.0013736E-02 0.2011204 at 130iterations 5.5774492E-03 0.1187859 at 140iterations 3.1185425E-03 6.9747925E-02 at 150iterations 1.7658257E-03 3.9166033E-02 at 160iterations 1.0224900E-03 2.2537231E-02 at 170iterations 6.1760494E-04 1.4012337E-02 at 180iterations finished qdiffx linear iterations at : 11:42:10 total time elapsed so far: 15.36000 # loops : 180 mean,max change (kT/e) : 6.1760494E-04 1.4012337E-02 energy calculations done at 15.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.63000 DelPhi exited at 11:42:11 15.636u 0.291s 0:16.36 97.3% 0+0k 0+0io 0pf+0w