Tue Oct 11 03:16:43 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 Tue Oct 11 2011 at 03:16:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3106 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5950292 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): -100.1150 -40.28600 ymin,ymax (A): 10.06000 66.03300 zmin,zma (A): -51.83700 6.954000 x,y,z range (A): 59.82900 55.97301 58.79100 scale (grids/A): 0.5950292 object centre (A): -70.20050 38.04650 -22.44150 number of atom coordinates read : 3106 total number of charged atoms : 2956 net assigned charge : -3.999990 assigned positive charge : 463.5811 centred at (gu) : 90.54782 89.48904 89.11745 assigned negative charge : -467.5820 centred at (gu) : 90.53431 89.51167 89.06384 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7534 nv = 96 ne = 84 npr = 58965 no. pairs analyzed = 58965 no. exposed pairs = 4658 no. arc points = 32614 no. surface atoms = 1543 nbur = 1563 mkacc time = 0.1400000 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 = 1.456000 m= 407 mr = 3551 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3282 ## 367 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9378 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2492450E-09 4.4563658E-10 midg,1,midg; midg,igrid,midg -6.5833367E-10 -2.0458275E-09 1,midg,midg; igrid,midg,midg -1.7257520E-09 -1.0513939E-09 gauss-seidel spectral radius is 0.9854453 estimated iterations to convergence 68 setup time was (sec) 0.5900000 now iterating at: 03:16:44 rms-change max change #iterations 0.1143907 17.90200 at 10iterations 9.5908605E-03 1.362476 at 20iterations 1.0065426E-03 0.1566772 at 30iterations 2.5897459E-04 3.6893845E-02 at 40iterations 1.0052513E-04 1.5390873E-02 at 50iterations finished qdiffx linear iterations at : 03:16:46 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.0052513E-04 1.5390873E-02 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 03:16:47 3.653u 0.200s 0:04.16 92.5% 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 Tue Oct 11 2011 at 03:16:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3106 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.785088 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): -100.1150 -40.28600 ymin,ymax (A): 10.06000 66.03300 zmin,zma (A): -51.83700 6.954000 x,y,z range (A): 59.82900 55.97301 58.79100 scale (grids/A): 1.785088 object centre (A): -70.20050 38.04650 -22.44150 number of atom coordinates read : 3106 total number of charged atoms : 2956 net assigned charge : -3.999990 assigned positive charge : 463.5811 centred at (gu) : 91.64275 88.46656 87.35155 assigned negative charge : -467.5820 centred at (gu) : 91.60254 88.53477 87.19122 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32614 grid for indexing accessible points = 1.400000 m= 27562 mr = 51733 m= 4147 mr = 18463 m= 191 mr = 2186 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 40609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 278 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 23019 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) : 0.5950292 object centre at (A) : -70.20050 38.04650 -22.44150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6747061E-02 -6.8203188E-03 midg,1,midg; midg,igrid,midg 3.3164853E-03 -7.6363073E-04 1,midg,midg; igrid,midg,midg 7.4715284E-03 5.4001198E-03 gauss-seidel spectral radius is 0.9985188 estimated iterations to convergence 206 setup time was (sec) 0.9600000 now iterating at: 03:16:48 rms-change max change #iterations 4.131435 186.1324 at 10iterations 1.874702 72.15644 at 20iterations 0.8461803 26.40192 at 30iterations 0.3819478 13.37410 at 40iterations 0.1734497 5.697802 at 50iterations 7.8304462E-02 2.872253 at 60iterations 3.5651330E-02 1.267475 at 70iterations 1.6183136E-02 0.5122128 at 80iterations 7.3387101E-03 0.2319354 at 90iterations 3.3777747E-03 0.1159191 at 100iterations 1.5756640E-03 5.1139832E-02 at 110iterations 7.6282449E-04 2.4739265E-02 at 120iterations finished qdiffx linear iterations at : 03:16:55 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 7.6282449E-04 2.4739265E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 03:16:56 8.266u 0.228s 0:09.15 92.6% 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 Tue Oct 11 2011 at 03:16:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3106 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.677631 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): -100.1150 -40.28600 ymin,ymax (A): 10.06000 66.03300 zmin,zma (A): -51.83700 6.954000 x,y,z range (A): 59.82900 55.97301 58.79100 scale (grids/A): 2.677631 object centre (A): -70.20050 38.04650 -22.44150 number of atom coordinates read : 3106 total number of charged atoms : 2956 net assigned charge : -3.999990 assigned positive charge : 463.5811 centred at (gu) : 92.46385 87.69964 86.02720 assigned negative charge : -467.5820 centred at (gu) : 92.40369 87.80208 85.78666 start vw surface at 0.1900000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 187263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32614 grid for indexing accessible points = 1.400000 m= 89077 mr = 126949 m= 31020 mr = 68347 m= 7191 mr = 23290 m= 839 mr = 4830 m= 31 mr = 417 m= 0 mr = 9 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.570000 number of dielectric boundary points 91579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 23630 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) : 1.785088 object centre at (A) : -70.20050 38.04650 -22.44150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3869132 3.0903993E-02 midg,1,midg; midg,igrid,midg 9.8672155E-03 -6.9851642E-03 1,midg,midg; igrid,midg,midg 0.2311623 1.2996864E-02 gauss-seidel spectral radius is 0.9992563 estimated iterations to convergence 289 setup time was (sec) 1.920000 now iterating at: 03:16:58 rms-change max change #iterations 10.34858 332.8541 at 10iterations 6.156389 180.1675 at 20iterations 3.627598 89.98834 at 30iterations 2.120144 48.29093 at 40iterations 1.234490 26.11272 at 50iterations 0.7156199 13.00849 at 60iterations 0.4142472 10.69936 at 70iterations 0.2392237 4.471627 at 80iterations 0.1383440 2.616257 at 90iterations 7.9724103E-02 1.536329 at 100iterations 4.5900870E-02 0.8893814 at 110iterations 2.6417747E-02 0.4825211 at 120iterations 1.5157867E-02 0.2843704 at 130iterations 8.7235030E-03 0.1498008 at 140iterations 5.0283843E-03 9.2262268E-02 at 150iterations 2.8965061E-03 5.1741153E-02 at 160iterations 1.6751026E-03 3.0164719E-02 at 170iterations 9.7790686E-04 1.8117428E-02 at 180iterations finished qdiffx linear iterations at : 03:17:10 total time elapsed so far: 13.27000 # loops : 180 mean,max change (kT/e) : 9.7790686E-04 1.8117428E-02 energy calculations done at 13.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.46000 DelPhi exited at 03:17:11 13.459u 0.291s 0:14.31 96.0% 0+0k 0+0io 0pf+0w