Mon Oct 10 19:32:27 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 Mon Oct 10 2011 at 19:32:27 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 = 2420 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: 0.6794541 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): -17.10100 35.29400 ymin,ymax (A): -10.16600 37.87400 zmin,zma (A): -2.312000 49.62400 x,y,z range (A): 52.39500 48.04000 51.93600 scale (grids/A): 0.6794541 object centre (A): 9.096501 13.85400 23.65600 number of atom coordinates read : 2420 total number of charged atoms : 2284 net assigned charge : 3.000010 assigned positive charge : 361.0928 centred at (gu) : 92.41063 91.28323 90.83199 assigned negative charge : -358.0935 centred at (gu) : 92.30984 91.49401 90.90208 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7773 nv = 96 ne = 84 npr = 48092 no. pairs analyzed = 48092 no. exposed pairs = 3265 no. arc points = 22565 no. surface atoms = 1087 nbur = 1333 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4187 m= 5 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2900000 number of dielectric boundary points 4002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2083 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8745 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8268197E-08 -9.3517913E-09 midg,1,midg; midg,igrid,midg 5.6676836E-08 -6.5975371E-08 1,midg,midg; igrid,midg,midg -1.0120603E-08 6.9536277E-08 gauss-seidel spectral radius is 0.9887599 estimated iterations to convergence 77 setup time was (sec) 0.5400000 now iterating at: 19:32:28 rms-change max change #iterations 0.1752674 24.96763 at 10iterations 1.9925268E-02 2.436722 at 20iterations 2.4965364E-03 0.3189354 at 30iterations 4.3172223E-04 6.5677643E-02 at 40iterations 1.2176217E-04 1.9203186E-02 at 50iterations finished qdiffx linear iterations at : 19:32:30 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.2176217E-04 1.9203186E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 19:32:32 3.386u 0.201s 0:04.42 80.9% 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 Mon Oct 10 2011 at 19:32:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 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: 2.038362 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): -17.10100 35.29400 ymin,ymax (A): -10.16600 37.87400 zmin,zma (A): -2.312000 49.62400 x,y,z range (A): 52.39500 48.04000 51.93600 scale (grids/A): 2.038362 object centre (A): 9.096501 13.85400 23.65600 number of atom coordinates read : 2420 total number of charged atoms : 2284 net assigned charge : 3.000010 assigned positive charge : 361.0928 centred at (gu) : 97.23122 93.84909 92.49561 assigned negative charge : -358.0935 centred at (gu) : 96.92921 94.48188 92.70622 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22565 grid for indexing accessible points = 1.400000 m= 32795 mr = 56328 m= 6780 mr = 24163 m= 663 mr = 4396 m= 21 mr = 313 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1082 time to turn everything in is 0.6200000 number of dielectric boundary points 37033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 18075 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) : 0.6794541 object centre at (A) : 9.096501 13.85400 23.65600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6005039E-02 2.3477251E-02 midg,1,midg; midg,igrid,midg 3.9242905E-02 -1.2731017E-03 1,midg,midg; igrid,midg,midg -1.0556157E-02 2.1320729E-02 gauss-seidel spectral radius is 0.9987896 estimated iterations to convergence 228 setup time was (sec) 0.9300000 now iterating at: 19:32:33 rms-change max change #iterations 4.674040 214.4698 at 10iterations 2.270145 78.31222 at 20iterations 1.111205 34.51266 at 30iterations 0.5436605 15.87833 at 40iterations 0.2660043 8.291654 at 50iterations 0.1303939 3.889524 at 60iterations 6.3828237E-02 1.916481 at 70iterations 3.1256404E-02 0.9396696 at 80iterations 1.5322937E-02 0.5357418 at 90iterations 7.5290711E-03 0.2275410 at 100iterations 3.7041821E-03 0.1054039 at 110iterations 1.8391123E-03 5.6110382E-02 at 120iterations finished qdiffx linear iterations at : 19:32:39 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 1.8391123E-03 5.6110382E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 19:32:40 7.553u 0.254s 0:08.45 92.3% 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 Mon Oct 10 2011 at 19:32:40 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 = 2420 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: 3.057544 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): -17.10100 35.29400 ymin,ymax (A): -10.16600 37.87400 zmin,zma (A): -2.312000 49.62400 x,y,z range (A): 52.39500 48.04000 51.93600 scale (grids/A): 3.057544 object centre (A): 9.096501 13.85400 23.65600 number of atom coordinates read : 2420 total number of charged atoms : 2284 net assigned charge : 3.000010 assigned positive charge : 361.0928 centred at (gu) : 100.8468 95.77339 93.74333 assigned negative charge : -358.0935 centred at (gu) : 100.3938 96.72286 94.05922 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 189180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22565 grid for indexing accessible points = 1.400000 m= 100476 mr = 136440 m= 42252 mr = 81720 m= 12902 mr = 34249 m= 2617 mr = 9813 m= 296 mr = 1832 m= 9 mr = 155 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 3419 time to turn everything in is 1.600000 number of dielectric boundary points 83524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 18272 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) : 2.038362 object centre at (A) : 9.096501 13.85400 23.65600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4274262 0.7486041 midg,1,midg; midg,igrid,midg 0.3034933 0.2549003 1,midg,midg; igrid,midg,midg -2.7427934E-02 0.1225333 gauss-seidel spectral radius is 0.9993016 estimated iterations to convergence 299 setup time was (sec) 1.940000 now iterating at: 19:32:43 rms-change max change #iterations 10.77345 488.6946 at 10iterations 6.457589 147.5998 at 20iterations 3.842408 74.37572 at 30iterations 2.282015 46.57397 at 40iterations 1.348769 30.83812 at 50iterations 0.7959532 14.54166 at 60iterations 0.4689405 7.985201 at 70iterations 0.2754607 4.846599 at 80iterations 0.1618199 2.769516 at 90iterations 9.4854511E-02 1.592384 at 100iterations 5.5651370E-02 0.9587317 at 110iterations 3.2636445E-02 0.5580518 at 120iterations 1.9090639E-02 0.3334007 at 130iterations 1.1177553E-02 0.1835995 at 140iterations 6.5482361E-03 0.1166725 at 150iterations 3.8366970E-03 6.3415527E-02 at 160iterations 2.2541201E-03 3.9503098E-02 at 170iterations 1.3386146E-03 2.4091721E-02 at 180iterations finished qdiffx linear iterations at : 19:32:53 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 1.3386146E-03 2.4091721E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 19:32:54 12.915u 0.222s 0:13.83 94.9% 0+0k 0+0io 0pf+0w