Wed Feb 15 08:57:22 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:57:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 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: 0.5708055 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 0.5708055 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2054 total number of charged atoms : 1927 net assigned charge : -1.999997 assigned positive charge : 271.8722 centred at (gu) : 91.99503 88.65961 88.47491 assigned negative charge : -273.8725 centred at (gu) : 91.99344 88.66325 88.66789 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 4536 nv = 96 ne = 84 npr = 43293 no. pairs analyzed = 43293 no. exposed pairs = 2765 no. arc points = 19548 no. surface atoms = 941 nbur = 1113 mkacc time = 0.1100000 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 = 1.540000 m= 236 mr = 2154 m= 0 mr = 18 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1898 ## 141 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 5612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2052158E-09 -1.5937788E-09 midg,1,midg; midg,igrid,midg -4.2065462E-10 -2.7916472E-10 1,midg,midg; igrid,midg,midg -2.2794613E-10 -5.2343191E-10 gauss-seidel spectral radius is 0.9840976 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 08:57:23 rms-change max change #iterations 6.7907460E-02 14.00606 at 10iterations 5.8635562E-03 1.175067 at 20iterations 1.3999935E-03 0.2668705 at 30iterations 6.2364043E-04 0.1181221 at 40iterations 2.8563317E-04 5.4073334E-02 at 50iterations finished qdiffx linear iterations at : 08:57:27 total time elapsed so far: 5.040000 # loops : 50 mean,max change (kT/e) : 2.8563317E-04 5.4073334E-02 energy calculations done at 5.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.220000 DelPhi exited at 08:57:28 5.225u 0.405s 0:06.18 90.9% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:57:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 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: 1.712417 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 1.712417 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2054 total number of charged atoms : 1927 net assigned charge : -1.999997 assigned positive charge : 271.8722 centred at (gu) : 95.98523 85.97900 85.42516 assigned negative charge : -273.8725 centred at (gu) : 95.98069 85.99010 86.00386 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 49302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19548 grid for indexing accessible points = 1.400000 m= 15679 mr = 31630 m= 2068 mr = 10448 m= 50 mr = 1056 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 23962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14997 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) : 0.5708055 object centre at (A) : -9.177502 -6.357000 49.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6587900E-02 -1.0946123E-02 midg,1,midg; midg,igrid,midg -2.8760650E-03 -1.0346362E-03 1,midg,midg; igrid,midg,midg -2.6626349E-04 -6.1321497E-04 gauss-seidel spectral radius is 0.9982605 estimated iterations to convergence 190 setup time was (sec) 0.7600000 now iterating at: 08:57:29 rms-change max change #iterations 2.767209 177.0236 at 10iterations 1.170479 55.04594 at 20iterations 0.4945606 22.15134 at 30iterations 0.2115144 9.070776 at 40iterations 8.9706160E-02 3.750662 at 50iterations 3.8422685E-02 1.588182 at 60iterations 1.6661258E-02 0.6644478 at 70iterations 7.6764384E-03 0.3094845 at 80iterations 3.9905603E-03 0.1785278 at 90iterations 2.4679082E-03 0.1062069 at 100iterations 1.7519301E-03 7.0041656E-02 at 110iterations 1.3216345E-03 5.1666260E-02 at 120iterations finished qdiffx linear iterations at : 08:57:41 total time elapsed so far: 12.50000 # loops : 120 mean,max change (kT/e) : 1.3216345E-03 5.1666260E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 08:57:41 12.665u 0.462s 0:13.39 97.9% 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 Wed Feb 15 2012 at 08:57:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 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: 2.568625 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 2.568625 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2054 total number of charged atoms : 1927 net assigned charge : -1.999997 assigned positive charge : 271.8722 centred at (gu) : 98.97779 83.96842 83.13780 assigned negative charge : -273.8725 centred at (gu) : 98.97121 83.98528 84.00581 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 114302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19548 grid for indexing accessible points = 1.400000 m= 51895 mr = 78115 m= 16910 mr = 39647 m= 3284 mr = 12491 m= 248 mr = 2208 m= 2 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 54059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 15408 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) : 1.712417 object centre at (A) : -9.177502 -6.357000 49.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3201461 -0.1560931 midg,1,midg; midg,igrid,midg -4.0709268E-02 -4.6189837E-03 1,midg,midg; igrid,midg,midg -3.5271156E-03 -1.3403212E-02 gauss-seidel spectral radius is 0.9991388 estimated iterations to convergence 269 setup time was (sec) 1.400000 now iterating at: 08:57:43 rms-change max change #iterations 7.069044 337.9791 at 10iterations 3.997463 107.1791 at 20iterations 2.235976 56.12892 at 30iterations 1.249064 33.55503 at 40iterations 0.6983633 18.90137 at 50iterations 0.3870451 9.036053 at 60iterations 0.2148660 6.098007 at 70iterations 0.1189410 3.234169 at 80iterations 6.5640636E-02 1.710356 at 90iterations 3.6398821E-02 0.8565845 at 100iterations 2.0093726E-02 0.4540873 at 110iterations 1.1159416E-02 0.2472386 at 120iterations 6.2636482E-03 0.1648865 at 130iterations 3.5805160E-03 9.0613306E-02 at 140iterations 2.1459986E-03 5.4435730E-02 at 150iterations 1.3856591E-03 3.6628723E-02 at 160iterations 9.8310830E-04 2.6268005E-02 at 170iterations 7.6135201E-04 1.8558502E-02 at 180iterations finished qdiffx linear iterations at : 08:58:02 total time elapsed so far: 20.47000 # loops : 180 mean,max change (kT/e) : 7.6135201E-04 1.8558502E-02 energy calculations done at 20.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.64000 DelPhi exited at 08:58:03 20.648u 0.477s 0:21.45 98.4% 0+0k 0+0io 0pf+0w