Tue Oct 11 06:13:46 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 Tue Oct 11 2011 at 06:13:46 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2228 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7019620 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): 16.92600 63.99500 ymin,ymax (A): -3.562000 33.43900 zmin,zma (A): 19.27600 69.99100 x,y,z range (A): 47.06900 37.00100 50.71500 scale (grids/A): 0.7019620 object centre (A): 40.46050 14.93850 44.63350 number of atom coordinates read : 2228 total number of charged atoms : 1923 net assigned charge : 6.039011 assigned positive charge : 315.1411 centred at (gu) : 90.66178 89.80843 89.89009 assigned negative charge : -309.1021 centred at (gu) : 90.80335 89.84093 89.85096 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6820 nv = 96 ne = 84 npr = 40788 no. pairs analyzed = 40788 no. exposed pairs = 2469 no. arc points = 16843 no. surface atoms = 835 nbur = 1393 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3889 m= 5 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1517 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7565 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8772750E-08 6.0793148E-08 midg,1,midg; midg,igrid,midg 6.1470281E-08 3.0014320E-08 1,midg,midg; igrid,midg,midg 9.2850513E-08 -1.9814349E-08 gauss-seidel spectral radius is 0.9894180 estimated iterations to convergence 79 setup time was (sec) 0.5200000 now iterating at: 06:13:46 rms-change max change #iterations 0.1946557 25.47236 at 10iterations 2.4114924E-02 2.949738 at 20iterations 3.2160734E-03 0.4318962 at 30iterations 5.1327283E-04 6.4842224E-02 at 40iterations 1.1161294E-04 1.4041901E-02 at 50iterations finished qdiffx linear iterations at : 06:13:49 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.1161294E-04 1.4041901E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 06:13:50 3.478u 0.184s 0:04.13 88.3% 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 Tue Oct 11 2011 at 06:13:50 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2228 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.105886 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): 16.92600 63.99500 ymin,ymax (A): -3.562000 33.43900 zmin,zma (A): 19.27600 69.99100 x,y,z range (A): 47.06900 37.00100 50.71500 scale (grids/A): 2.105886 object centre (A): 40.46050 14.93850 44.63350 number of atom coordinates read : 2228 total number of charged atoms : 1923 net assigned charge : 6.039011 assigned positive charge : 315.1411 centred at (gu) : 91.98541 89.42534 89.67016 assigned negative charge : -309.1021 centred at (gu) : 92.41028 89.52297 89.55298 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 72600 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16843 grid for indexing accessible points = 1.400000 m= 28405 mr = 51638 m= 5209 mr = 21447 m= 484 mr = 3433 m= 10 mr = 275 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 29915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15161 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) : 0.7019620 object centre at (A) : 40.46050 14.93850 44.63350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4269046E-02 4.7932938E-02 midg,1,midg; midg,igrid,midg 2.5998261E-02 1.2250014E-02 1,midg,midg; igrid,midg,midg 3.0634310E-02 1.4777251E-02 gauss-seidel spectral radius is 0.9988112 estimated iterations to convergence 230 setup time was (sec) 0.8900000 now iterating at: 06:13:51 rms-change max change #iterations 4.549595 277.1389 at 10iterations 2.247562 88.69307 at 20iterations 1.103161 37.69034 at 30iterations 0.5476688 17.12512 at 40iterations 0.2704873 8.643065 at 50iterations 0.1337252 4.209244 at 60iterations 6.6015594E-02 1.949791 at 70iterations 3.2724205E-02 1.068069 at 80iterations 1.6233340E-02 0.5221176 at 90iterations 8.0847172E-03 0.2678680 at 100iterations 4.0673311E-03 0.1260910 at 110iterations 2.0654162E-03 6.1279297E-02 at 120iterations finished qdiffx linear iterations at : 06:13:58 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 2.0654162E-03 6.1279297E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 06:13:58 7.908u 0.214s 0:08.51 95.2% 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 Tue Oct 11 2011 at 06:13:58 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2228 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.158829 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): 16.92600 63.99500 ymin,ymax (A): -3.562000 33.43900 zmin,zma (A): 19.27600 69.99100 x,y,z range (A): 47.06900 37.00100 50.71500 scale (grids/A): 3.158829 object centre (A): 40.46050 14.93850 44.63350 number of atom coordinates read : 2228 total number of charged atoms : 1923 net assigned charge : 6.039011 assigned positive charge : 315.1411 centred at (gu) : 92.97814 89.13799 89.50522 assigned negative charge : -309.1021 centred at (gu) : 93.61551 89.28450 89.32948 start vw surface at 0.1600000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 167404 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16843 grid for indexing accessible points = 1.400000 m= 89446 mr = 124314 m= 35402 mr = 74444 m= 9809 mr = 28915 m= 1966 mr = 7581 m= 242 mr = 1467 m= 3 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.800000 number of dielectric boundary points 67401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 15383 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) : 2.105886 object centre at (A) : 40.46050 14.93850 44.63350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2780616 0.3401759 midg,1,midg; midg,igrid,midg 0.2280125 0.1044589 1,midg,midg; igrid,midg,midg 0.2519020 0.2993503 gauss-seidel spectral radius is 0.9992892 estimated iterations to convergence 296 setup time was (sec) 2.130000 now iterating at: 06:14:01 rms-change max change #iterations 10.11666 324.8732 at 10iterations 5.946065 127.8317 at 20iterations 3.486696 65.31770 at 30iterations 2.048594 45.57338 at 40iterations 1.197874 22.87551 at 50iterations 0.7004896 14.02171 at 60iterations 0.4083618 7.575002 at 70iterations 0.2393024 4.304234 at 80iterations 0.1393713 2.483086 at 90iterations 8.1484050E-02 1.442564 at 100iterations 4.7769208E-02 0.8466721 at 110iterations 2.8089592E-02 0.4813232 at 120iterations 1.6707433E-02 0.3046684 at 130iterations 1.0053940E-02 0.1904602 at 140iterations 6.2391981E-03 0.1290207 at 150iterations 3.9907452E-03 7.6961517E-02 at 160iterations 2.7064267E-03 5.4775238E-02 at 170iterations 1.9312125E-03 4.0885925E-02 at 180iterations finished qdiffx linear iterations at : 06:14:11 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 1.9312125E-03 4.0885925E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 06:14:12 13.179u 0.231s 0:13.91 96.3% 0+0k 0+0io 0pf+0w