Mon Oct 10 13:55:59 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 13:55:59 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2706 !!! WARNING: ASL 104 has a net charge of -0.1000 !!! WARNING: HIT 236 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: 0.5764902 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): -21.92900 39.82400 ymin,ymax (A): -9.697000 43.46100 zmin,zma (A): -1.654000 52.57000 x,y,z range (A): 61.75300 53.15800 54.22400 scale (grids/A): 0.5764902 object centre (A): 8.947501 16.88200 25.45800 number of atom coordinates read : 2706 total number of charged atoms : 2561 net assigned charge : 11.91402 assigned positive charge : 400.0061 centred at (gu) : 92.10994 90.50411 86.56446 assigned negative charge : -388.0925 centred at (gu) : 92.15269 90.51936 86.33459 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5914 nv = 96 ne = 84 npr = 52783 no. pairs analyzed = 52783 no. exposed pairs = 4051 no. arc points = 29029 no. surface atoms = 1345 nbur = 1361 mkacc time = 0.1200000 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 = 1.484000 m= 259 mr = 2517 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2843 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7464782E-09 2.7937732E-09 midg,1,midg; midg,igrid,midg 2.3894964E-09 2.4374631E-09 1,midg,midg; igrid,midg,midg 1.9388393E-09 2.7596869E-09 gauss-seidel spectral radius is 0.9844615 estimated iterations to convergence 66 setup time was (sec) 0.5500000 now iterating at: 13:55:59 rms-change max change #iterations 8.9394115E-02 18.57171 at 10iterations 6.8384763E-03 1.104872 at 20iterations 5.2635674E-04 8.3317757E-02 at 30iterations 4.4541801E-05 6.6452026E-03 at 40iterations 4.9817554E-06 6.5517426E-04 at 50iterations finished qdiffx linear iterations at : 13:56:02 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 4.9817554E-06 6.5517426E-04 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 13:56:03 3.390u 0.149s 0:04.22 83.6% 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 Mon Oct 10 2011 at 13:56:03 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2706 !!! WARNING: ASL 104 has a net charge of -0.1000 !!! WARNING: HIT 236 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.729471 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): -21.92900 39.82400 ymin,ymax (A): -9.697000 43.46100 zmin,zma (A): -1.654000 52.57000 x,y,z range (A): 61.75300 53.15800 54.22400 scale (grids/A): 1.729471 object centre (A): 8.947501 16.88200 25.45800 number of atom coordinates read : 2706 total number of charged atoms : 2561 net assigned charge : 11.91402 assigned positive charge : 400.0061 centred at (gu) : 96.32951 91.51179 79.69284 assigned negative charge : -388.0925 centred at (gu) : 96.45771 91.55767 79.00372 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29029 grid for indexing accessible points = 1.400000 m= 18496 mr = 37848 m= 2216 mr = 11516 m= 77 mr = 1005 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 33475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 19843 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) : 0.5764902 object centre at (A) : 8.947501 16.88200 25.45800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7858108E-04 1.8511217E-02 midg,1,midg; midg,igrid,midg 1.9438127E-02 1.9901097E-02 1,midg,midg; igrid,midg,midg -1.1487888E-02 2.3099491E-02 gauss-seidel spectral radius is 0.9983629 estimated iterations to convergence 196 setup time was (sec) 0.7500000 now iterating at: 13:56:04 rms-change max change #iterations 3.516722 167.0255 at 10iterations 1.512139 70.16197 at 20iterations 0.6566435 25.49638 at 30iterations 0.2846085 12.32154 at 40iterations 0.1232386 4.499827 at 50iterations 5.3364381E-02 1.817177 at 60iterations 2.3220541E-02 0.8737078 at 70iterations 1.0084564E-02 0.3514156 at 80iterations 4.3678866E-03 0.1609764 at 90iterations 1.9022920E-03 6.7988396E-02 at 100iterations 8.2596834E-04 2.9830456E-02 at 110iterations 3.5947436E-04 1.3123512E-02 at 120iterations finished qdiffx linear iterations at : 13:56:10 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 3.5947436E-04 1.3123512E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 13:56:11 7.482u 0.186s 0:08.06 95.0% 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 13:56:11 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2706 !!! WARNING: ASL 104 has a net charge of -0.1000 !!! WARNING: HIT 236 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: 2.594206 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): -21.92900 39.82400 ymin,ymax (A): -9.697000 43.46100 zmin,zma (A): -1.654000 52.57000 x,y,z range (A): 61.75300 53.15800 54.22400 scale (grids/A): 2.594206 object centre (A): 8.947501 16.88200 25.45800 number of atom coordinates read : 2706 total number of charged atoms : 2561 net assigned charge : 11.91402 assigned positive charge : 400.0061 centred at (gu) : 99.49429 92.26753 74.53912 assigned negative charge : -388.0925 centred at (gu) : 99.68648 92.33656 73.50567 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 145809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29029 grid for indexing accessible points = 1.400000 m= 62461 mr = 94148 m= 18721 mr = 45900 m= 3441 mr = 13092 m= 302 mr = 2084 m= 13 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 75395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 20476 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) : 1.729471 object centre at (A) : 8.947501 16.88200 25.45800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1447163E-02 0.2070980 midg,1,midg; midg,igrid,midg 0.2899532 0.2486105 1,midg,midg; igrid,midg,midg -0.4910434 0.2461362 gauss-seidel spectral radius is 0.9991944 estimated iterations to convergence 278 setup time was (sec) 1.470000 now iterating at: 13:56:13 rms-change max change #iterations 9.062005 314.7051 at 10iterations 5.288132 144.6317 at 20iterations 3.048802 81.26797 at 30iterations 1.744961 49.31958 at 40iterations 0.9914036 24.04281 at 50iterations 0.5637811 14.23561 at 60iterations 0.3187610 7.440513 at 70iterations 0.1799362 4.654076 at 80iterations 0.1013231 2.406054 at 90iterations 5.6956392E-02 1.294298 at 100iterations 3.2085054E-02 0.6943693 at 110iterations 1.8018613E-02 0.4240875 at 120iterations 1.0113930E-02 0.2154675 at 130iterations 5.6684138E-03 0.1207228 at 140iterations 3.1839719E-03 7.4214935E-02 at 150iterations 1.7869917E-03 3.6060333E-02 at 160iterations 1.0032783E-03 2.1502495E-02 at 170iterations 5.6141708E-04 1.1905193E-02 at 180iterations finished qdiffx linear iterations at : 13:56:23 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 5.6141708E-04 1.1905193E-02 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 13:56:24 12.305u 0.220s 0:12.90 97.0% 0+0k 0+0io 0pf+0w