Mon Oct 10 14:11:14 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 14:11:15 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3383 !!! WARNING: HIR 12 has a net charge of 0.5140 !!! WARNING: HIR 14 has a net charge of 0.5140 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: HIR 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6164609 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): 35.34700 85.18400 ymin,ymax (A): 26.23500 83.98400 zmin,zma (A): -3.295000 45.73100 x,y,z range (A): 49.83700 57.74900 49.02600 scale (grids/A): 0.6164609 object centre (A): 60.26550 55.10950 21.21800 number of atom coordinates read : 3383 total number of charged atoms : 3249 net assigned charge : -6.443966 assigned positive charge : 521.1119 centred at (gu) : 91.19597 89.55458 90.74899 assigned negative charge : -527.5574 centred at (gu) : 91.03027 89.61404 90.77409 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8337 nv = 96 ne = 84 npr = 71103 no. pairs analyzed = 71103 no. exposed pairs = 3761 no. arc points = 25624 no. surface atoms = 1283 nbur = 2100 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 470 mr = 5000 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 118 time to turn everything in is 0.3300000 number of dielectric boundary points 3747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2531 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10436 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3856350E-09 -8.0894216E-09 midg,1,midg; midg,igrid,midg 1.2650538E-11 -8.7864702E-09 1,midg,midg; igrid,midg,midg -1.4241565E-08 1.1128897E-08 gauss-seidel spectral radius is 0.9864298 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 14:11:15 rms-change max change #iterations 0.1499769 22.86476 at 10iterations 1.3600772E-02 1.728095 at 20iterations 1.3452016E-03 0.1713505 at 30iterations 1.8689445E-04 3.1207085E-02 at 40iterations 4.6336576E-05 8.7718964E-03 at 50iterations finished qdiffx linear iterations at : 14:11:18 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 4.6336576E-05 8.7718964E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 14:11:18 3.348u 0.214s 0:03.89 91.2% 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 Mon Oct 10 2011 at 14:11:18 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3383 !!! WARNING: HIR 12 has a net charge of 0.5140 !!! WARNING: HIR 14 has a net charge of 0.5140 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: HIR 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.849383 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): 35.34700 85.18400 ymin,ymax (A): 26.23500 83.98400 zmin,zma (A): -3.295000 45.73100 x,y,z range (A): 49.83700 57.74900 49.02600 scale (grids/A): 1.849383 object centre (A): 60.26550 55.10950 21.21800 number of atom coordinates read : 3383 total number of charged atoms : 3249 net assigned charge : -6.443966 assigned positive charge : 521.1119 centred at (gu) : 93.58684 88.66291 92.24588 assigned negative charge : -527.5574 centred at (gu) : 93.09022 88.84131 92.32172 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 89190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25624 grid for indexing accessible points = 1.400000 m= 36368 mr = 64642 m= 6439 mr = 28693 m= 291 mr = 4381 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 4422 time to turn everything in is 0.6300000 number of dielectric boundary points 34498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 25475 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) : 0.6164609 object centre at (A) : 60.26550 55.10950 21.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8426785E-02 -2.6160736E-02 midg,1,midg; midg,igrid,midg 2.9989746E-03 -3.9891582E-02 1,midg,midg; igrid,midg,midg -2.9051678E-02 1.8937448E-02 gauss-seidel spectral radius is 0.9986158 estimated iterations to convergence 213 setup time was (sec) 0.9300000 now iterating at: 14:11:20 rms-change max change #iterations 4.758516 167.2113 at 10iterations 2.221585 76.63591 at 20iterations 1.035034 29.38548 at 30iterations 0.4825902 13.77578 at 40iterations 0.2258459 7.440781 at 50iterations 0.1056567 2.852444 at 60iterations 4.9107894E-02 1.403927 at 70iterations 2.2991925E-02 0.6629257 at 80iterations 1.0754338E-02 0.3042558 at 90iterations 5.0384244E-03 0.1479263 at 100iterations 2.3730646E-03 7.3900223E-02 at 110iterations 1.1243535E-03 3.3262253E-02 at 120iterations finished qdiffx linear iterations at : 14:11:26 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.1243535E-03 3.3262253E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 14:11:27 7.799u 0.221s 0:08.50 94.2% 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 Mon Oct 10 2011 at 14:11:27 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3383 !!! WARNING: HIR 12 has a net charge of 0.5140 !!! WARNING: HIR 14 has a net charge of 0.5140 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: HIR 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.774074 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): 35.34700 85.18400 ymin,ymax (A): 26.23500 83.98400 zmin,zma (A): -3.295000 45.73100 x,y,z range (A): 49.83700 57.74900 49.02600 scale (grids/A): 2.774074 object centre (A): 60.26550 55.10950 21.21800 number of atom coordinates read : 3383 total number of charged atoms : 3249 net assigned charge : -6.443966 assigned positive charge : 521.1119 centred at (gu) : 95.37996 87.99409 93.36870 assigned negative charge : -527.5574 centred at (gu) : 94.63510 88.26180 93.48242 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 206215 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25624 grid for indexing accessible points = 1.400000 m= 112544 mr = 155400 m= 46836 mr = 95363 m= 11866 mr = 40017 m= 1378 mr = 9397 m= 56 mr = 855 m= 0 mr = 20 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 15135 time to turn everything in is 1.620000 number of dielectric boundary points 77843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 25990 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) : 1.849383 object centre at (A) : 60.26550 55.10950 21.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2752611 -0.2923084 midg,1,midg; midg,igrid,midg -0.1378713 -0.2747769 1,midg,midg; igrid,midg,midg -0.2782454 0.2493349 gauss-seidel spectral radius is 0.9992593 estimated iterations to convergence 290 setup time was (sec) 1.930000 now iterating at: 14:11:29 rms-change max change #iterations 11.17761 344.1439 at 10iterations 6.527662 159.2138 at 20iterations 3.792994 99.15544 at 30iterations 2.199301 40.27153 at 40iterations 1.275056 27.88403 at 50iterations 0.7362645 13.29586 at 60iterations 0.4246325 7.148959 at 70iterations 0.2444473 4.702740 at 80iterations 0.1411229 2.420359 at 90iterations 8.1085436E-02 1.295619 at 100iterations 4.6740167E-02 0.7472382 at 110iterations 2.6940800E-02 0.4459658 at 120iterations 1.5517743E-02 0.2861328 at 130iterations 8.9796968E-03 0.1557884 at 140iterations 5.2096574E-03 8.4294319E-02 at 150iterations 3.0352345E-03 5.0969481E-02 at 160iterations 1.7948387E-03 3.2548904E-02 at 170iterations 1.0823357E-03 2.0095348E-02 at 180iterations finished qdiffx linear iterations at : 14:11:40 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 1.0823357E-03 2.0095348E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 14:11:41 12.781u 0.245s 0:14.40 90.4% 0+0k 0+0io 0pf+0w