Sun Oct 9 12:36:33 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 Sun Oct 9 2011 at 12:36:33 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 0.6914232 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): -4.664000 43.67300 ymin,ymax (A): -13.83000 37.65800 zmin,zma (A): 2.163000 45.31700 x,y,z range (A): 48.33700 51.48800 43.15400 scale (grids/A): 0.6914232 object centre (A): 19.50450 11.91400 23.74000 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 362.3892 centred at (gu) : 89.02599 90.53801 90.39532 assigned negative charge : -358.8896 centred at (gu) : 89.02612 90.69711 90.44729 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7614 nv = 96 ne = 84 npr = 47629 no. pairs analyzed = 47629 no. exposed pairs = 2964 no. arc points = 20807 no. surface atoms = 985 nbur = 1381 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4222 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.2000000 number of dielectric boundary points 3795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1914 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8624 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7856235E-08 -1.3762852E-10 midg,1,midg; midg,igrid,midg 7.3863319E-08 -4.8352828E-08 1,midg,midg; igrid,midg,midg 2.4880718E-08 1.7023396E-08 gauss-seidel spectral radius is 0.9891313 estimated iterations to convergence 78 setup time was (sec) 0.3900000 now iterating at: 12:36:33 rms-change max change #iterations 0.1964395 27.29370 at 10iterations 2.3919355E-02 3.274643 at 20iterations 3.1338071E-03 0.4378471 at 30iterations 6.0613459E-04 9.1697693E-02 at 40iterations 1.7341241E-04 2.8160095E-02 at 50iterations finished qdiffx linear iterations at : 12:36:36 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.7341241E-04 2.8160095E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 12:36:36 3.471u 0.165s 0:03.90 93.0% 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 12:36:37 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 2.074270 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): -4.664000 43.67300 ymin,ymax (A): -13.83000 37.65800 zmin,zma (A): 2.163000 45.31700 x,y,z range (A): 48.33700 51.48800 43.15400 scale (grids/A): 2.074270 object centre (A): 19.50450 11.91400 23.74000 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 362.3892 centred at (gu) : 87.07755 91.61372 91.18545 assigned negative charge : -358.8896 centred at (gu) : 87.07817 92.09120 91.34161 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 81017 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20807 grid for indexing accessible points = 1.400000 m= 30915 mr = 56176 m= 5323 mr = 22977 m= 454 mr = 3408 m= 3 mr = 240 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1868 time to turn everything in is 0.3900000 number of dielectric boundary points 34911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17629 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) : 0.6914232 object centre at (A) : 19.50450 11.91400 23.74000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3525876E-02 1.3372967E-02 midg,1,midg; midg,igrid,midg 2.2150002E-02 -4.2449404E-02 1,midg,midg; igrid,midg,midg 3.2992091E-02 -6.0372348E-03 gauss-seidel spectral radius is 0.9988192 estimated iterations to convergence 230 setup time was (sec) 0.6300000 now iterating at: 12:36:37 rms-change max change #iterations 4.824106 199.7690 at 10iterations 2.367893 82.39668 at 20iterations 1.168154 37.57165 at 30iterations 0.5787235 18.82590 at 40iterations 0.2855183 9.191841 at 50iterations 0.1407806 4.230659 at 60iterations 6.9497257E-02 2.141336 at 70iterations 3.4564048E-02 1.068456 at 80iterations 1.7119283E-02 0.5312443 at 90iterations 8.6130854E-03 0.2438240 at 100iterations 4.3325950E-03 0.1253433 at 110iterations 2.2266610E-03 7.2574615E-02 at 120iterations finished qdiffx linear iterations at : 12:36:45 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 2.2266610E-03 7.2574615E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 12:36:45 8.168u 0.230s 0:08.65 96.9% 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 12:36:45 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 3.111405 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): -4.664000 43.67300 ymin,ymax (A): -13.83000 37.65800 zmin,zma (A): 2.163000 45.31700 x,y,z range (A): 48.33700 51.48800 43.15400 scale (grids/A): 3.111405 object centre (A): 19.50450 11.91400 23.74000 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 362.3892 centred at (gu) : 85.61634 92.42052 91.77820 assigned negative charge : -358.8896 centred at (gu) : 85.61720 93.13678 92.01234 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 186967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20807 grid for indexing accessible points = 1.400000 m= 98270 mr = 136022 m= 37554 mr = 80723 m= 9657 mr = 30331 m= 1811 mr = 7263 m= 171 mr = 1338 m= 0 mr = 98 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 5924 time to turn everything in is 1.230000 number of dielectric boundary points 78655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 17796 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) : 2.074270 object centre at (A) : 19.50450 11.91400 23.74000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4651832 3.6741361E-02 midg,1,midg; midg,igrid,midg 0.5180861 -0.4608390 1,midg,midg; igrid,midg,midg 0.3215183 -0.2865309 gauss-seidel spectral radius is 0.9992974 estimated iterations to convergence 298 setup time was (sec) 1.480000 now iterating at: 12:36:47 rms-change max change #iterations 10.86471 441.5984 at 10iterations 6.423991 127.1186 at 20iterations 3.792918 87.63129 at 30iterations 2.241503 42.52539 at 40iterations 1.318287 29.23473 at 50iterations 0.7743724 14.51184 at 60iterations 0.4543996 8.141020 at 70iterations 0.2665547 4.517474 at 80iterations 0.1562545 2.975708 at 90iterations 9.1435812E-02 1.640308 at 100iterations 5.3591985E-02 1.124367 at 110iterations 3.1481348E-02 0.5117903 at 120iterations 1.8640528E-02 0.3449440 at 130iterations 1.1119611E-02 0.1973267 at 140iterations 6.7552058E-03 0.1267662 at 150iterations 4.2272243E-03 8.7471008E-02 at 160iterations 2.7769848E-03 6.5486908E-02 at 170iterations 1.9299523E-03 4.2755127E-02 at 180iterations finished qdiffx linear iterations at : 12:36:59 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 1.9299523E-03 4.2755127E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.51000 DelPhi exited at 12:36:59 13.509u 0.229s 0:14.03 97.7% 0+0k 0+0io 0pf+0w