Sun Oct 9 12:59:27 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 Sun Oct 9 2011 at 12:59:27 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 = 2359 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: 0.6938624 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): -5.253000 44.40000 ymin,ymax (A): -14.40200 36.90500 zmin,zma (A): 1.427000 45.74200 x,y,z range (A): 49.65300 51.30700 44.31500 scale (grids/A): 0.6938624 object centre (A): 19.57350 11.25150 23.58450 number of atom coordinates read : 2359 total number of charged atoms : 2218 net assigned charge : 3.500019 assigned positive charge : 359.2310 centred at (gu) : 89.21800 91.19114 90.62398 assigned negative charge : -355.7316 centred at (gu) : 89.24596 91.35061 90.67332 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7905 nv = 96 ne = 84 npr = 46408 no. pairs analyzed = 46408 no. exposed pairs = 2991 no. arc points = 21199 no. surface atoms = 1005 nbur = 1354 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 490 mr = 4395 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2081 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8798 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7597751E-08 1.8144065E-09 midg,1,midg; midg,igrid,midg 6.8683889E-08 -5.7444854E-08 1,midg,midg; igrid,midg,midg 3.9349292E-08 9.2654462E-09 gauss-seidel spectral radius is 0.9892110 estimated iterations to convergence 78 setup time was (sec) 0.4800000 now iterating at: 12:59:27 rms-change max change #iterations 0.1963978 26.54048 at 10iterations 2.3765462E-02 3.482780 at 20iterations 3.1638611E-03 0.4121513 at 30iterations 6.0287950E-04 9.3952179E-02 at 40iterations 1.7125640E-04 2.7980804E-02 at 50iterations finished qdiffx linear iterations at : 12:59:30 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.7125640E-04 2.7980804E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 12:59:30 3.078u 0.139s 0:03.49 91.6% 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 Sun Oct 9 2011 at 12:59:30 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 = 2359 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: 2.081587 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): -5.253000 44.40000 ymin,ymax (A): -14.40200 36.90500 zmin,zma (A): 1.427000 45.74200 x,y,z range (A): 49.65300 51.30700 44.31500 scale (grids/A): 2.081587 object centre (A): 19.57350 11.25150 23.58450 number of atom coordinates read : 2359 total number of charged atoms : 2218 net assigned charge : 3.500019 assigned positive charge : 359.2310 centred at (gu) : 87.65347 93.57285 91.87160 assigned negative charge : -355.7316 centred at (gu) : 87.73753 94.05155 92.01985 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21199 grid for indexing accessible points = 1.400000 m= 33310 mr = 58073 m= 6125 mr = 25089 m= 533 mr = 4010 m= 14 mr = 274 m= 0 mr = 1 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 36041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17587 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) : 0.6938624 object centre at (A) : 19.57350 11.25150 23.58450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6849404E-02 1.1215601E-02 midg,1,midg; midg,igrid,midg 1.7080547E-02 -4.5352872E-02 1,midg,midg; igrid,midg,midg 6.0124550E-02 -2.0749565E-02 gauss-seidel spectral radius is 0.9988298 estimated iterations to convergence 231 setup time was (sec) 0.8700000 now iterating at: 12:59:31 rms-change max change #iterations 4.839797 288.7542 at 10iterations 2.374186 75.78743 at 20iterations 1.175481 36.46844 at 30iterations 0.5799942 19.00267 at 40iterations 0.2885586 8.355957 at 50iterations 0.1430652 4.509216 at 60iterations 7.1108200E-02 1.946421 at 70iterations 3.5195641E-02 0.9598541 at 80iterations 1.7633256E-02 0.5566788 at 90iterations 8.8882521E-03 0.2879791 at 100iterations 4.5551220E-03 0.1525650 at 110iterations 2.4233630E-03 8.5803986E-02 at 120iterations finished qdiffx linear iterations at : 12:59:38 total time elapsed so far: 7.000000 # loops : 120 mean,max change (kT/e) : 2.4233630E-03 8.5803986E-02 energy calculations done at 7.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.200000 DelPhi exited at 12:59:38 7.198u 0.158s 0:07.73 94.9% 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 Sun Oct 9 2011 at 12:59:38 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 = 2359 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: 3.122381 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): -5.253000 44.40000 ymin,ymax (A): -14.40200 36.90500 zmin,zma (A): 1.427000 45.74200 x,y,z range (A): 49.65300 51.30700 44.31500 scale (grids/A): 3.122381 object centre (A): 19.57350 11.25150 23.58450 number of atom coordinates read : 2359 total number of charged atoms : 2218 net assigned charge : 3.500019 assigned positive charge : 359.2310 centred at (gu) : 86.48015 95.35920 92.80726 assigned negative charge : -355.7316 centred at (gu) : 86.60629 96.07730 93.02969 start vw surface at 0.1500000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 192040 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21199 grid for indexing accessible points = 1.400000 m= 103876 mr = 139742 m= 41825 mr = 85966 m= 11534 mr = 34129 m= 2283 mr = 8808 m= 246 mr = 1702 m= 11 mr = 167 m= 0 mr = 4 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.870000 number of dielectric boundary points 81297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 17744 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) : 2.081587 object centre at (A) : 19.57350 11.25150 23.58450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4645496 -2.3131466E-02 midg,1,midg; midg,igrid,midg 0.3296292 -0.5596896 1,midg,midg; igrid,midg,midg 0.8228633 -0.4420063 gauss-seidel spectral radius is 0.9993005 estimated iterations to convergence 298 setup time was (sec) 2.150000 now iterating at: 12:59:40 rms-change max change #iterations 10.86671 467.5504 at 10iterations 6.446986 125.7402 at 20iterations 3.818723 79.03946 at 30iterations 2.255257 39.84573 at 40iterations 1.333090 22.55014 at 50iterations 0.7843472 13.51734 at 60iterations 0.4603253 9.431702 at 70iterations 0.2707721 4.919819 at 80iterations 0.1591572 3.127537 at 90iterations 9.3201689E-02 1.584141 at 100iterations 5.5002276E-02 1.066282 at 110iterations 3.2338891E-02 0.5205419 at 120iterations 1.9258669E-02 0.3642006 at 130iterations 1.1636737E-02 0.2194214 at 140iterations 7.2296006E-03 0.1474304 at 150iterations 4.6889158E-03 9.3529299E-02 at 160iterations 3.2353376E-03 7.3520660E-02 at 170iterations 2.3855276E-03 5.0117493E-02 at 180iterations finished qdiffx linear iterations at : 12:59:50 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 2.3855276E-03 5.0117493E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 12:59:51 12.307u 0.174s 0:12.99 95.9% 0+0k 0+0io 0pf+0w