Tue Oct 11 03:21:52 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 03:21:52 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1155 !!! 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: 0.7461591 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): -6.678000 29.35700 ymin,ymax (A): 1.330000 40.36900 zmin,zma (A): -1.473000 46.23800 x,y,z range (A): 36.03500 39.03900 47.71100 scale (grids/A): 0.7461591 object centre (A): 11.33950 20.84950 22.38250 number of atom coordinates read : 1155 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 89.70985 89.16800 88.41677 assigned negative charge : -172.6512 centred at (gu) : 89.42044 89.14661 88.42062 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4390 nv = 96 ne = 84 npr = 22192 no. pairs analyzed = 22192 no. exposed pairs = 1498 no. arc points = 10937 no. surface atoms = 506 nbur = 649 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 287 mr = 2222 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 3.9999999E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1100000 number of dielectric boundary points 2394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 944 ## 75 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 4538 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5172128E-07 8.2523968E-08 midg,1,midg; midg,igrid,midg 1.1401422E-07 1.0750847E-07 1,midg,midg; igrid,midg,midg -7.7080529E-08 2.7082686E-07 gauss-seidel spectral radius is 0.9905419 estimated iterations to convergence 84 setup time was (sec) 0.3400000 now iterating at: 03:21:52 rms-change max change #iterations 0.1853813 31.26819 at 10iterations 2.4611626E-02 3.758210 at 20iterations 3.2853002E-03 0.5265961 at 30iterations 4.4291111E-04 7.2603226E-02 at 40iterations 6.0044626E-05 9.9954605E-03 at 50iterations finished qdiffx linear iterations at : 03:21:55 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 6.0044626E-05 9.9954605E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 03:21:56 3.669u 0.222s 0:04.34 89.4% 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 03:21:56 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1155 !!! 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: 2.238477 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): -6.678000 29.35700 ymin,ymax (A): 1.330000 40.36900 zmin,zma (A): -1.473000 46.23800 x,y,z range (A): 36.03500 39.03900 47.71100 scale (grids/A): 2.238477 object centre (A): 11.33950 20.84950 22.38250 number of atom coordinates read : 1155 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 89.12962 87.50396 85.25043 assigned negative charge : -172.6512 centred at (gu) : 88.26160 87.44021 85.26208 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 45740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10937 grid for indexing accessible points = 1.400000 m= 17203 mr = 29722 m= 3476 mr = 12748 m= 365 mr = 2327 m= 18 mr = 223 m= 0 mr = 13 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 21769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 8461 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) : 0.7461591 object centre at (A) : 11.33950 20.84950 22.38250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5642526E-02 9.3262810E-03 midg,1,midg; midg,igrid,midg 4.3622386E-02 3.6246315E-02 1,midg,midg; igrid,midg,midg -2.5001466E-02 4.0606868E-02 gauss-seidel spectral radius is 0.9988491 estimated iterations to convergence 233 setup time was (sec) 0.5100000 now iterating at: 03:21:57 rms-change max change #iterations 3.717618 180.4115 at 10iterations 1.853791 95.72571 at 20iterations 0.9249251 33.90752 at 30iterations 0.4594508 17.90167 at 40iterations 0.2283603 8.281273 at 50iterations 0.1131358 4.404732 at 60iterations 5.6209475E-02 2.211600 at 70iterations 2.8009998E-02 1.073402 at 80iterations 1.3937202E-02 0.4888992 at 90iterations 6.8998360E-03 0.2560480 at 100iterations 3.4214789E-03 0.1354194 at 110iterations 1.7006947E-03 6.0712814E-02 at 120iterations finished qdiffx linear iterations at : 03:22:04 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 1.7006947E-03 6.0712814E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 03:22:05 8.199u 0.284s 0:08.94 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 03:22:05 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1155 !!! 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: 3.357716 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): -6.678000 29.35700 ymin,ymax (A): 1.330000 40.36900 zmin,zma (A): -1.473000 46.23800 x,y,z range (A): 36.03500 39.03900 47.71100 scale (grids/A): 3.357716 object centre (A): 11.33950 20.84950 22.38250 number of atom coordinates read : 1155 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 88.69440 86.25591 82.87565 assigned negative charge : -172.6512 centred at (gu) : 87.39244 86.16040 82.89320 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 105544 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10937 grid for indexing accessible points = 1.400000 m= 53104 mr = 72070 m= 21798 mr = 43080 m= 6561 mr = 17875 m= 1409 mr = 5179 m= 229 mr = 1107 m= 26 mr = 166 m= 4 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 49173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8100000 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) : 2.238477 object centre at (A) : 11.33950 20.84950 22.38250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2080268 5.9088182E-02 midg,1,midg; midg,igrid,midg 0.3921094 0.3190559 1,midg,midg; igrid,midg,midg -0.1943504 0.2803216 gauss-seidel spectral radius is 0.9992968 estimated iterations to convergence 298 setup time was (sec) 0.9500000 now iterating at: 03:22:06 rms-change max change #iterations 8.115810 404.4086 at 10iterations 4.732574 127.6020 at 20iterations 2.747382 72.87680 at 30iterations 1.586595 35.11394 at 40iterations 0.9243131 20.35130 at 50iterations 0.5357615 12.10104 at 60iterations 0.3116755 6.510920 at 70iterations 0.1802396 3.736435 at 80iterations 0.1047481 2.179619 at 90iterations 6.0787123E-02 1.450918 at 100iterations 3.5170630E-02 0.7534904 at 110iterations 2.0529902E-02 0.5197716 at 120iterations 1.1907124E-02 0.2404556 at 130iterations 6.8935542E-03 0.1624775 at 140iterations 4.0024118E-03 8.7203979E-02 at 150iterations 2.3243544E-03 4.9335480E-02 at 160iterations 1.3477856E-03 2.8972626E-02 at 170iterations 7.8259397E-04 1.7456055E-02 at 180iterations finished qdiffx linear iterations at : 03:22:18 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 7.8259397E-04 1.7456055E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 03:22:18 12.455u 0.281s 0:13.09 97.2% 0+0k 0+0io 0pf+0w