Sat Oct 15 12:53:44 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 Sat Oct 15 2011 at 12:53:44 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 = 3509 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: 0.5256164 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): -15.45400 51.73900 ymin,ymax (A): -26.20100 41.52900 zmin,zma (A): 3.104000 55.53000 x,y,z range (A): 67.19300 67.73000 52.42600 scale (grids/A): 0.5256164 object centre (A): 18.14250 7.664001 29.31700 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : 2.000018 assigned positive charge : 519.3887 centred at (gu) : 90.19415 90.11475 90.99194 assigned negative charge : -517.3911 centred at (gu) : 90.19369 90.20856 90.96162 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6606 nv = 96 ne = 84 npr = 66951 no. pairs analyzed = 66951 no. exposed pairs = 5132 no. arc points = 36832 no. surface atoms = 1702 nbur = 1807 mkacc time = 0.1800000 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 = 1.624000 m= 238 mr = 2990 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3516 ## 448 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0428938E-11 2.0626000E-10 midg,1,midg; midg,igrid,midg 3.6757294E-10 -2.8769556E-10 1,midg,midg; igrid,midg,midg 4.9715981E-11 5.8135611E-11 gauss-seidel spectral radius is 0.9814178 estimated iterations to convergence 61 setup time was (sec) 0.7000000 now iterating at: 12:53:45 rms-change max change #iterations 6.3452363E-02 10.22235 at 10iterations 3.8327272E-03 0.6940250 at 20iterations 2.5419806E-04 4.4795990E-02 at 30iterations 2.7027769E-05 6.2961578E-03 at 40iterations 5.2380210E-06 1.2903214E-03 at 50iterations finished qdiffx linear iterations at : 12:53:50 total time elapsed so far: 5.300000 # loops : 50 mean,max change (kT/e) : 5.2380210E-06 1.2903214E-03 energy calculations done at 5.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.480000 DelPhi exited at 12:53:50 5.489u 0.438s 0:06.31 93.6% 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 Sat Oct 15 2011 at 12:53:50 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 = 3509 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: 1.576849 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): -15.45400 51.73900 ymin,ymax (A): -26.20100 41.52900 zmin,zma (A): 3.104000 55.53000 x,y,z range (A): 67.19300 67.73000 52.42600 scale (grids/A): 1.576849 object centre (A): 18.14250 7.664001 29.31700 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : 2.000018 assigned positive charge : 519.3887 centred at (gu) : 90.58142 90.34344 92.97491 assigned negative charge : -517.3911 centred at (gu) : 90.58075 90.62524 92.88451 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72679 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36832 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20975 mr = 45817 m= 2098 mr = 13098 m= 42 mr = 849 m= 0 mr = 1 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.6400000 number of dielectric boundary points 36029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 374 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 25579 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) : 0.5256164 object centre at (A) : 18.14250 7.664001 29.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8054730E-03 3.7556581E-04 midg,1,midg; midg,igrid,midg 2.6095407E-02 6.9141947E-03 1,midg,midg; igrid,midg,midg 4.8522284E-04 1.1779709E-02 gauss-seidel spectral radius is 0.9981369 estimated iterations to convergence 184 setup time was (sec) 1.020000 now iterating at: 12:53:52 rms-change max change #iterations 3.375966 169.1957 at 10iterations 1.384266 50.32274 at 20iterations 0.5690640 22.02708 at 30iterations 0.2343641 10.12971 at 40iterations 9.6672289E-02 3.260403 at 50iterations 3.9793566E-02 1.606283 at 60iterations 1.6420612E-02 0.6035557 at 70iterations 6.7636012E-03 0.2375946 at 80iterations 2.7870738E-03 0.1031265 at 90iterations 1.1495184E-03 4.0714264E-02 at 100iterations 4.7544713E-04 1.7943621E-02 at 110iterations 1.9644565E-04 6.8244934E-03 at 120iterations finished qdiffx linear iterations at : 12:54:03 total time elapsed so far: 12.44000 # loops : 120 mean,max change (kT/e) : 1.9644565E-04 6.8244934E-03 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 12:54:04 12.619u 0.515s 0:13.56 96.7% 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 Sat Oct 15 2011 at 12:54:04 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 = 3509 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: 2.365274 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): -15.45400 51.73900 ymin,ymax (A): -26.20100 41.52900 zmin,zma (A): 3.104000 55.53000 x,y,z range (A): 67.19300 67.73000 52.42600 scale (grids/A): 2.365274 object centre (A): 18.14250 7.664001 29.31700 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : 2.000018 assigned positive charge : 519.3887 centred at (gu) : 90.87199 90.51497 94.46185 assigned negative charge : -517.3911 centred at (gu) : 90.87103 90.93763 94.32678 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 169275 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36832 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 72067 mr = 113846 m= 20014 mr = 53359 m= 3007 mr = 13979 m= 155 mr = 1758 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 1.560000 number of dielectric boundary points 81539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 26845 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) : 1.576849 object centre at (A) : 18.14250 7.664001 29.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7484234E-02 -3.2544469E-03 midg,1,midg; midg,igrid,midg 0.4899723 -1.8293409E-02 1,midg,midg; igrid,midg,midg 1.5403423E-02 0.3922362 gauss-seidel spectral radius is 0.9991513 estimated iterations to convergence 271 setup time was (sec) 2.000000 now iterating at: 12:54:07 rms-change max change #iterations 9.171904 324.2642 at 10iterations 5.287582 172.5292 at 20iterations 3.015316 77.20486 at 30iterations 1.704245 44.85731 at 40iterations 0.9609662 25.27541 at 50iterations 0.5368925 16.84351 at 60iterations 0.3007736 6.775490 at 70iterations 0.1674550 4.188832 at 80iterations 9.3007050E-02 2.466773 at 90iterations 5.1661052E-02 1.159622 at 100iterations 2.8608637E-02 0.6485357 at 110iterations 1.5831172E-02 0.3361664 at 120iterations 8.7583195E-03 0.1787995 at 130iterations 4.8523066E-03 0.1061401 at 140iterations 2.6880505E-03 5.2484989E-02 at 150iterations 1.4863469E-03 2.9910088E-02 at 160iterations 8.2200050E-04 1.6067505E-02 at 170iterations 4.5452709E-04 9.6786022E-03 at 180iterations finished qdiffx linear iterations at : 12:54:27 total time elapsed so far: 22.00000 # loops : 180 mean,max change (kT/e) : 4.5452709E-04 9.6786022E-03 energy calculations done at 22.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.17000 DelPhi exited at 12:54:27 22.179u 0.558s 0:23.14 98.1% 0+0k 0+0io 0pf+0w