Tue Oct 11 05:23:31 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 05:23:32 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG8 870 has a net charge of 1.4000 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: 0.6905113 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): 19.77200 63.06600 ymin,ymax (A): -3.545000 33.56300 zmin,zma (A): 20.29000 71.84600 x,y,z range (A): 43.29400 37.10800 51.55600 scale (grids/A): 0.6905113 object centre (A): 41.41900 15.00900 46.06800 number of atom coordinates read : 2247 total number of charged atoms : 1936 net assigned charge : 8.425010 assigned positive charge : 314.5370 centred at (gu) : 90.20231 89.66950 89.27357 assigned negative charge : -306.1122 centred at (gu) : 90.36844 89.68466 89.26424 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6762 nv = 96 ne = 84 npr = 41073 no. pairs analyzed = 41073 no. exposed pairs = 2498 no. arc points = 16953 no. surface atoms = 845 nbur = 1402 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3889 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1670 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7553 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0910373E-08 4.3857490E-08 midg,1,midg; midg,igrid,midg 5.5801085E-08 3.9767958E-08 1,midg,midg; igrid,midg,midg 9.7184873E-08 -8.7802192E-09 gauss-seidel spectral radius is 0.9890703 estimated iterations to convergence 78 setup time was (sec) 0.4700000 now iterating at: 05:23:32 rms-change max change #iterations 0.1801859 26.92728 at 10iterations 2.1245424E-02 3.700317 at 20iterations 2.4996859E-03 0.3293800 at 30iterations 3.0769111E-04 4.3884277E-02 at 40iterations 4.0176968E-05 5.1956177E-03 at 50iterations finished qdiffx linear iterations at : 05:23:35 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 4.0176968E-05 5.1956177E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 05:23:35 3.210u 0.210s 0:03.75 91.2% 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 05:23:35 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG8 870 has a net charge of 1.4000 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: 2.071534 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): 19.77200 63.06600 ymin,ymax (A): -3.545000 33.56300 zmin,zma (A): 20.29000 71.84600 x,y,z range (A): 43.29400 37.10800 51.55600 scale (grids/A): 2.071534 object centre (A): 41.41900 15.00900 46.06800 number of atom coordinates read : 2247 total number of charged atoms : 1936 net assigned charge : 8.425010 assigned positive charge : 314.5370 centred at (gu) : 90.60728 89.00848 87.82060 assigned negative charge : -306.1122 centred at (gu) : 91.10537 89.05402 87.79271 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16953 grid for indexing accessible points = 1.400000 m= 28659 mr = 50796 m= 5479 mr = 21892 m= 474 mr = 3659 m= 11 mr = 262 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 0.5300000 number of dielectric boundary points 29315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 15348 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) : 0.6905113 object centre at (A) : 41.41900 15.00900 46.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8302291E-02 4.3385644E-02 midg,1,midg; midg,igrid,midg 2.4039874E-02 1.4344107E-02 1,midg,midg; igrid,midg,midg 4.0438447E-02 1.5845491E-02 gauss-seidel spectral radius is 0.9987778 estimated iterations to convergence 226 setup time was (sec) 0.8200000 now iterating at: 05:23:36 rms-change max change #iterations 4.370604 215.3514 at 10iterations 2.135773 81.27062 at 20iterations 1.034077 36.50054 at 30iterations 0.5086129 17.59920 at 40iterations 0.2478054 7.897566 at 50iterations 0.1207529 3.947893 at 60iterations 5.8787335E-02 1.940951 at 70iterations 2.8812116E-02 0.9021759 at 80iterations 1.4076516E-02 0.4634380 at 90iterations 6.9073671E-03 0.1947708 at 100iterations 3.3845336E-03 0.1006044 at 110iterations 1.6668999E-03 5.2573264E-02 at 120iterations finished qdiffx linear iterations at : 05:23:43 total time elapsed so far: 7.200000 # loops : 120 mean,max change (kT/e) : 1.6668999E-03 5.2573264E-02 energy calculations done at 7.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 05:23:43 7.383u 0.219s 0:08.01 94.7% 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 05:23:43 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG8 870 has a net charge of 1.4000 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: 3.107301 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): 19.77200 63.06600 ymin,ymax (A): -3.545000 33.56300 zmin,zma (A): 20.29000 71.84600 x,y,z range (A): 43.29400 37.10800 51.55600 scale (grids/A): 3.107301 object centre (A): 41.41900 15.00900 46.06800 number of atom coordinates read : 2247 total number of charged atoms : 1936 net assigned charge : 8.425010 assigned positive charge : 314.5370 centred at (gu) : 90.91092 88.51268 86.73086 assigned negative charge : -306.1122 centred at (gu) : 91.65811 88.58100 86.68912 start vw surface at 0.1600000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 164431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16953 grid for indexing accessible points = 1.400000 m= 89623 mr = 122395 m= 36158 mr = 74745 m= 10125 mr = 29780 m= 1900 mr = 7909 m= 205 mr = 1400 m= 2 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.640000 number of dielectric boundary points 66071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 15488 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) : 2.071534 object centre at (A) : 41.41900 15.00900 46.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4589679 0.3019314 midg,1,midg; midg,igrid,midg 0.2138908 0.1212090 1,midg,midg; igrid,midg,midg 0.3335108 0.2960315 gauss-seidel spectral radius is 0.9992805 estimated iterations to convergence 294 setup time was (sec) 1.940000 now iterating at: 05:23:46 rms-change max change #iterations 9.890744 436.9450 at 10iterations 5.833786 165.1054 at 20iterations 3.428963 69.25235 at 30iterations 2.008283 40.95001 at 40iterations 1.174426 28.26894 at 50iterations 0.6864334 16.51768 at 60iterations 0.4000921 8.319528 at 70iterations 0.2340713 4.268478 at 80iterations 0.1364663 2.355284 at 90iterations 7.9379313E-02 1.463065 at 100iterations 4.6324521E-02 0.8615294 at 110iterations 2.7048282E-02 0.5698185 at 120iterations 1.5771978E-02 0.2821159 at 130iterations 9.2884824E-03 0.1736183 at 140iterations 5.5133896E-03 0.1174068 at 150iterations 3.3171840E-03 6.1630249E-02 at 160iterations 2.0488398E-03 4.2526245E-02 at 170iterations 1.3135979E-03 2.8816223E-02 at 180iterations finished qdiffx linear iterations at : 05:23:56 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 1.3135979E-03 2.8816223E-02 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 05:23:56 12.228u 0.229s 0:12.77 97.4% 0+0k 0+0io 0pf+0w