Sun Oct 9 19:39:06 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 Sun Oct 9 2011 at 19:39:06 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3164 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5719978 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): -11.16800 51.07000 ymin,ymax (A): -11.99400 41.27500 zmin,zma (A): 19.76300 76.23100 x,y,z range (A): 62.23800 53.26900 56.46800 scale (grids/A): 0.5719978 object centre (A): 19.95100 14.64050 47.99700 number of atom coordinates read : 3164 total number of charged atoms : 3010 net assigned charge : 3.240032 assigned positive charge : 486.0099 centred at (gu) : 90.55721 89.46545 87.65108 assigned negative charge : -482.7711 centred at (gu) : 90.48573 89.55774 87.64704 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6986 nv = 96 ne = 84 npr = 61143 no. pairs analyzed = 61143 no. exposed pairs = 4288 no. arc points = 30266 no. surface atoms = 1436 nbur = 1728 mkacc time = 0.2000000 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= 347 mr = 3515 m= 4 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2959 ## 330 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8726 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5889089E-10 3.4471864E-10 midg,1,midg; midg,igrid,midg 2.4668632E-09 -1.0327492E-09 1,midg,midg; igrid,midg,midg -6.9049033E-10 2.0570179E-09 gauss-seidel spectral radius is 0.9842498 estimated iterations to convergence 65 setup time was (sec) 0.7300000 now iterating at: 19:39:07 rms-change max change #iterations 9.3282074E-02 15.42469 at 10iterations 7.1752332E-03 1.039465 at 20iterations 5.4490147E-04 9.3734741E-02 at 30iterations 4.7402322E-05 7.3366165E-03 at 40iterations 1.0429655E-05 1.4097691E-03 at 50iterations finished qdiffx linear iterations at : 19:39:11 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 1.0429655E-05 1.4097691E-03 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 19:39:12 4.590u 0.416s 0:05.33 93.8% 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 Sun Oct 9 2011 at 19:39:12 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3164 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.715994 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): -11.16800 51.07000 ymin,ymax (A): -11.99400 41.27500 zmin,zma (A): 19.76300 76.23100 x,y,z range (A): 62.23800 53.26900 56.46800 scale (grids/A): 1.715994 object centre (A): 19.95100 14.64050 47.99700 number of atom coordinates read : 3164 total number of charged atoms : 3010 net assigned charge : 3.240032 assigned positive charge : 486.0099 centred at (gu) : 91.67113 88.39550 82.95253 assigned negative charge : -482.7711 centred at (gu) : 91.45683 88.67290 82.94080 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 76401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30266 grid for indexing accessible points = 1.400000 m= 25520 mr = 51135 m= 3206 mr = 17255 m= 107 mr = 1505 m= 0 mr = 14 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 35325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 23303 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) : 0.5719978 object centre at (A) : 19.95100 14.64050 47.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5179455E-02 5.7189856E-03 midg,1,midg; midg,igrid,midg 1.9563776E-02 -1.0371388E-02 1,midg,midg; igrid,midg,midg -6.2259394E-03 5.0248071E-03 gauss-seidel spectral radius is 0.9983891 estimated iterations to convergence 198 setup time was (sec) 1.140000 now iterating at: 19:39:13 rms-change max change #iterations 3.892455 176.5121 at 10iterations 1.709100 61.31958 at 20iterations 0.7539714 27.41360 at 30iterations 0.3314419 11.62343 at 40iterations 0.1458590 5.390251 at 50iterations 6.4386874E-02 2.226395 at 60iterations 2.8313458E-02 1.029085 at 70iterations 1.2481488E-02 0.5081577 at 80iterations 5.5118864E-03 0.1850252 at 90iterations 2.4309768E-03 8.1237793E-02 at 100iterations 1.0883408E-03 3.9103508E-02 at 110iterations 5.0719612E-04 1.8939495E-02 at 120iterations finished qdiffx linear iterations at : 19:39:22 total time elapsed so far: 10.50000 # loops : 120 mean,max change (kT/e) : 5.0719612E-04 1.8939495E-02 energy calculations done at 10.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.72000 DelPhi exited at 19:39:23 10.726u 0.441s 0:11.46 97.3% 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 Sun Oct 9 2011 at 19:39:23 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3164 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.573990 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): -11.16800 51.07000 ymin,ymax (A): -11.99400 41.27500 zmin,zma (A): 19.76300 76.23100 x,y,z range (A): 62.23800 53.26900 56.46800 scale (grids/A): 2.573990 object centre (A): 19.95100 14.64050 47.99700 number of atom coordinates read : 3164 total number of charged atoms : 3010 net assigned charge : 3.240032 assigned positive charge : 486.0099 centred at (gu) : 92.50652 87.59312 79.42852 assigned negative charge : -482.7711 centred at (gu) : 92.18522 88.00923 79.41109 start vw surface at 0.1600000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 177078 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30266 grid for indexing accessible points = 1.400000 m= 85040 mr = 125279 m= 27255 mr = 66280 m= 5132 mr = 20146 m= 505 mr = 3212 m= 16 mr = 279 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.990000 number of dielectric boundary points 79827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 24043 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) : 1.715994 object centre at (A) : 19.95100 14.64050 47.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2951893 7.3183961E-02 midg,1,midg; midg,igrid,midg 0.2784274 -0.2087097 1,midg,midg; igrid,midg,midg 0.1250548 0.1096810 gauss-seidel spectral radius is 0.9992116 estimated iterations to convergence 281 setup time was (sec) 2.360000 now iterating at: 19:39:26 rms-change max change #iterations 9.992729 286.2273 at 10iterations 5.881831 147.4418 at 20iterations 3.410554 79.41354 at 30iterations 1.972970 45.31760 at 40iterations 1.132721 26.75771 at 50iterations 0.6470586 13.90524 at 60iterations 0.3696946 7.954291 at 70iterations 0.2110438 4.325752 at 80iterations 0.1195858 2.328907 at 90iterations 6.8090543E-02 1.415024 at 100iterations 3.8730804E-02 0.7681351 at 110iterations 2.1973513E-02 0.5532532 at 120iterations 1.2509885E-02 0.2357922 at 130iterations 7.1384129E-03 0.1447430 at 140iterations 4.1217124E-03 8.3585739E-02 at 150iterations 2.4275149E-03 4.8942566E-02 at 160iterations 1.5021203E-03 3.2511711E-02 at 170iterations 9.9901203E-04 2.1883011E-02 at 180iterations finished qdiffx linear iterations at : 19:39:41 total time elapsed so far: 17.94000 # loops : 180 mean,max change (kT/e) : 9.9901203E-04 2.1883011E-02 energy calculations done at 17.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.16000 DelPhi exited at 19:39:42 18.164u 0.482s 0:18.93 98.4% 0+0k 0+0io 0pf+0w