Tue Oct 11 08:24:40 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 08:24:40 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1177 !!! WARNING: HIT 60 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= 9.9999998E-03 grid size : 179 scale,in grids/A, set to be: 0.7316973 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): -6.660000 31.94200 ymin,ymax (A): 1.052000 39.81000 zmin,zma (A): -2.458000 46.19600 x,y,z range (A): 38.60200 38.75800 48.65400 scale (grids/A): 0.7316973 object centre (A): 12.64100 20.43100 21.86900 number of atom coordinates read : 1177 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.5651 centred at (gu) : 88.85358 89.41885 88.81031 assigned negative charge : -173.0511 centred at (gu) : 88.57887 89.40076 88.81139 start vw surface at 3.9999999E-02 fill in re-entrant regions at 5.0000001E-02 boundary points on vw surface= 4302 nv = 96 ne = 84 npr = 22890 no. pairs analyzed = 22890 no. exposed pairs = 1486 no. arc points = 10899 no. surface atoms = 500 nbur = 677 mkacc time = 2.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 235 mr = 2225 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 4.0000003E-02 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 9.0000004E-02 number of dielectric boundary points 2273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 890 ## 80 charges are in solution ## iepsmp to db, and charging done at 0.1500000 number of grid points assigned charge 4402 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0349851E-07 6.6270431E-08 midg,1,midg; midg,igrid,midg 8.2603592E-08 8.1841982E-08 1,midg,midg; igrid,midg,midg -6.0809072E-08 1.6616946E-07 gauss-seidel spectral radius is 0.9901725 estimated iterations to convergence 82 setup time was (sec) 0.2700000 now iterating at: 08:24:41 rms-change max change #iterations 0.1710564 31.55463 at 10iterations 2.2575030E-02 3.498092 at 20iterations 2.8442254E-03 0.4688988 at 30iterations 3.7494212E-04 6.7481995E-02 at 40iterations 4.8520520E-05 8.9035034E-03 at 50iterations finished qdiffx linear iterations at : 08:24:44 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 4.8520520E-05 8.9035034E-03 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 08:24:45 3.221u 0.195s 0:04.64 73.4% 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 08:24:45 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1177 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.195092 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): -6.660000 31.94200 ymin,ymax (A): 1.052000 39.81000 zmin,zma (A): -2.458000 46.19600 x,y,z range (A): 38.60200 38.75800 48.65400 scale (grids/A): 2.195092 object centre (A): 12.64100 20.43100 21.86900 number of atom coordinates read : 1177 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.5651 centred at (gu) : 86.56079 88.25677 86.43103 assigned negative charge : -173.0511 centred at (gu) : 85.73665 88.20245 86.43438 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 44751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10899 grid for indexing accessible points = 1.400000 m= 16503 mr = 29268 m= 3018 mr = 12322 m= 255 mr = 2043 m= 15 mr = 143 m= 0 mr = 7 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 652 time to turn everything in is 0.2300000 number of dielectric boundary points 20759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8449 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) : 0.7316973 object centre at (A) : 12.64100 20.43100 21.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0961826E-02 1.0038093E-02 midg,1,midg; midg,igrid,midg 3.1868748E-02 3.0976404E-02 1,midg,midg; igrid,midg,midg -2.5867429E-02 3.8438745E-02 gauss-seidel spectral radius is 0.9988110 estimated iterations to convergence 230 setup time was (sec) 0.4300000 now iterating at: 08:24:46 rms-change max change #iterations 3.624127 186.9630 at 10iterations 1.783346 85.86295 at 20iterations 0.8732704 34.93246 at 30iterations 0.4291203 15.64278 at 40iterations 0.2113828 9.819935 at 50iterations 0.1036690 3.840374 at 60iterations 5.0998881E-02 2.290318 at 70iterations 2.5083421E-02 0.9408278 at 80iterations 1.2264750E-02 0.4771156 at 90iterations 6.0741198E-03 0.3165474 at 100iterations 2.9787757E-03 0.1181126 at 110iterations 1.4678495E-03 5.6819916E-02 at 120iterations finished qdiffx linear iterations at : 08:24:53 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 1.4678495E-03 5.6819916E-02 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 08:24:53 7.533u 0.204s 0:08.24 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 Tue Oct 11 2011 at 08:24:53 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1177 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.292638 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): -6.660000 31.94200 ymin,ymax (A): 1.052000 39.81000 zmin,zma (A): -2.458000 46.19600 x,y,z range (A): 38.60200 38.75800 48.65400 scale (grids/A): 3.292638 object centre (A): 12.64100 20.43100 21.86900 number of atom coordinates read : 1177 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.5651 centred at (gu) : 84.84124 87.38507 84.64651 assigned negative charge : -173.0511 centred at (gu) : 83.60492 87.30376 84.65160 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 102912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10899 grid for indexing accessible points = 1.400000 m= 51618 mr = 70868 m= 20665 mr = 42086 m= 5666 mr = 16954 m= 1008 mr = 4425 m= 151 mr = 796 m= 15 mr = 124 m= 0 mr = 7 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1950 time to turn everything in is 0.7000000 number of dielectric boundary points 46775 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 8488 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) : 2.195092 object centre at (A) : 12.64100 20.43100 21.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1252699 0.1182687 midg,1,midg; midg,igrid,midg 0.3013535 0.2574086 1,midg,midg; igrid,midg,midg -0.2181213 0.2868370 gauss-seidel spectral radius is 0.9992824 estimated iterations to convergence 295 setup time was (sec) 0.9200000 now iterating at: 08:24:55 rms-change max change #iterations 7.880305 324.8505 at 10iterations 4.568246 122.6405 at 20iterations 2.636625 64.12709 at 30iterations 1.520426 33.63751 at 40iterations 0.8777992 18.33967 at 50iterations 0.5058779 11.80426 at 60iterations 0.2928098 7.313484 at 70iterations 0.1690503 3.510444 at 80iterations 9.7309962E-02 2.876527 at 90iterations 5.6253061E-02 1.150659 at 100iterations 3.2417893E-02 0.7150822 at 110iterations 1.8824641E-02 0.4125938 at 120iterations 1.0836865E-02 0.2375040 at 130iterations 6.2517892E-03 0.1364365 at 140iterations 3.6214401E-03 9.2200279E-02 at 150iterations 2.0856413E-03 4.5852661E-02 at 160iterations 1.2077149E-03 2.5650024E-02 at 170iterations 6.9678068E-04 1.4690399E-02 at 180iterations finished qdiffx linear iterations at : 08:25:06 total time elapsed so far: 11.81000 # loops : 180 mean,max change (kT/e) : 6.9678068E-04 1.4690399E-02 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 08:25:06 11.937u 0.240s 0:12.68 95.9% 0+0k 0+0io 0pf+0w