Mon Oct 10 18:36:18 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 18:36:19 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2363 !!! WARNING: HIR 257 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7029461 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): -41.96100 4.183000 ymin,ymax (A): 57.29500 107.9390 zmin,zma (A): -20.47300 29.52700 x,y,z range (A): 46.14400 50.64400 50.00000 scale (grids/A): 0.7029461 object centre (A): -18.88900 82.61700 4.527000 number of atom coordinates read : 2363 total number of charged atoms : 2226 net assigned charge : 1.014005 assigned positive charge : 354.7240 centred at (gu) : 89.24287 87.64883 88.62451 assigned negative charge : -353.7106 centred at (gu) : 89.17465 87.77659 88.59158 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7980 nv = 96 ne = 84 npr = 48145 no. pairs analyzed = 48145 no. exposed pairs = 2975 no. arc points = 20880 no. surface atoms = 1004 nbur = 1359 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 571 mr = 4473 m= 3 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.1900000 number of dielectric boundary points 3971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1830 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8850 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3480173E-08 1.7610301E-08 midg,1,midg; midg,igrid,midg 1.1257947E-07 -3.6604057E-08 1,midg,midg; igrid,midg,midg -3.2702363E-08 3.4955136E-08 gauss-seidel spectral radius is 0.9894871 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 18:36:19 rms-change max change #iterations 0.2114981 34.78711 at 10iterations 2.5758743E-02 3.331371 at 20iterations 3.0875364E-03 0.3734341 at 30iterations 3.8613233E-04 4.6815872E-02 at 40iterations 5.0966359E-05 6.5355301E-03 at 50iterations finished qdiffx linear iterations at : 18:36:22 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 5.0966359E-05 6.5355301E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 18:36:23 3.404u 0.172s 0:04.14 86.2% 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 18:36:23 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2363 !!! WARNING: HIR 257 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: 2.108838 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): -41.96100 4.183000 ymin,ymax (A): 57.29500 107.9390 zmin,zma (A): -20.47300 29.52700 x,y,z range (A): 46.14400 50.64400 50.00000 scale (grids/A): 2.108838 object centre (A): -18.88900 82.61700 4.527000 number of atom coordinates read : 2363 total number of charged atoms : 2226 net assigned charge : 1.014005 assigned positive charge : 354.7240 centred at (gu) : 87.72793 82.94595 85.87309 assigned negative charge : -353.7106 centred at (gu) : 87.52382 83.32971 85.77454 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20880 grid for indexing accessible points = 1.400000 m= 34345 mr = 58087 m= 7593 mr = 26268 m= 678 mr = 5294 m= 19 mr = 309 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1096 time to turn everything in is 0.4300000 number of dielectric boundary points 36402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17708 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) : 0.7029461 object centre at (A) : -18.88900 82.61700 4.527000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1613901E-03 1.5699102E-02 midg,1,midg; midg,igrid,midg 4.1599102E-02 -2.4729822E-02 1,midg,midg; igrid,midg,midg -1.7101329E-03 1.8262351E-02 gauss-seidel spectral radius is 0.9988499 estimated iterations to convergence 233 setup time was (sec) 0.6500000 now iterating at: 18:36:24 rms-change max change #iterations 4.933621 214.6925 at 10iterations 2.443614 78.96795 at 20iterations 1.219349 40.66207 at 30iterations 0.6091068 17.76935 at 40iterations 0.3040845 9.115352 at 50iterations 0.1513918 4.569351 at 60iterations 7.5349182E-02 2.479111 at 70iterations 3.7603412E-02 1.015085 at 80iterations 1.8830644E-02 0.5455360 at 90iterations 9.3722241E-03 0.2536240 at 100iterations 4.6821903E-03 0.1506405 at 110iterations 2.3376753E-03 6.5245152E-02 at 120iterations finished qdiffx linear iterations at : 18:36:31 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 2.3376753E-03 6.5245152E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 18:36:31 7.970u 0.190s 0:08.43 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 Mon Oct 10 2011 at 18:36:31 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2363 !!! WARNING: HIR 257 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.163257 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): -41.96100 4.183000 ymin,ymax (A): 57.29500 107.9390 zmin,zma (A): -20.47300 29.52700 x,y,z range (A): 46.14400 50.64400 50.00000 scale (grids/A): 3.163257 object centre (A): -18.88900 82.61700 4.527000 number of atom coordinates read : 2363 total number of charged atoms : 2226 net assigned charge : 1.014005 assigned positive charge : 354.7240 centred at (gu) : 86.59184 79.41879 83.80951 assigned negative charge : -353.7106 centred at (gu) : 86.28566 79.99459 83.66172 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 192664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20880 grid for indexing accessible points = 1.400000 m= 104394 mr = 139683 m= 46243 mr = 86748 m= 14658 mr = 38789 m= 2888 mr = 11630 m= 247 mr = 2045 m= 5 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 3840 time to turn everything in is 1.300000 number of dielectric boundary points 82071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 17808 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) : 2.108838 object centre at (A) : -18.88900 82.61700 4.527000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5744182E-02 0.8359727 midg,1,midg; midg,igrid,midg 0.3006262 -5.5106815E-02 1,midg,midg; igrid,midg,midg 1.2035222E-02 9.5121637E-02 gauss-seidel spectral radius is 0.9993130 estimated iterations to convergence 301 setup time was (sec) 1.550000 now iterating at: 18:36:33 rms-change max change #iterations 11.10981 426.0951 at 10iterations 6.618561 145.6368 at 20iterations 3.927767 67.75663 at 30iterations 2.321872 47.13346 at 40iterations 1.375741 23.24866 at 50iterations 0.8116665 14.06539 at 60iterations 0.4776990 8.903291 at 70iterations 0.2807886 4.625138 at 80iterations 0.1651098 2.726148 at 90iterations 9.7029321E-02 1.519150 at 100iterations 5.7051264E-02 0.9318767 at 110iterations 3.3494104E-02 0.5434799 at 120iterations 1.9670578E-02 0.3116946 at 130iterations 1.1582246E-02 0.1779270 at 140iterations 6.8290038E-03 0.1142874 at 150iterations 4.0290928E-03 7.0346832E-02 at 160iterations 2.3946699E-03 3.9539337E-02 at 170iterations 1.4340858E-03 2.4797440E-02 at 180iterations finished qdiffx linear iterations at : 18:36:45 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 1.4340858E-03 2.4797440E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 18:36:45 13.312u 0.219s 0:14.06 96.1% 0+0k 0+0io 0pf+0w