Wed Feb 15 08:58:04 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:58:04 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 = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6044655 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): -18.12800 23.22900 ymin,ymax (A): -15.99700 32.48900 zmin,zma (A): 18.22900 77.12400 x,y,z range (A): 41.35700 48.48600 58.89500 scale (grids/A): 0.6044655 object centre (A): 2.550500 8.246001 47.67650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000007 assigned positive charge : 313.9017 centred at (gu) : 89.77329 88.97313 88.82716 assigned negative charge : -311.9023 centred at (gu) : 89.71577 89.05069 89.08790 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5688 nv = 96 ne = 84 npr = 49905 no. pairs analyzed = 49905 no. exposed pairs = 3186 no. arc points = 22215 no. surface atoms = 1091 nbur = 1236 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 2704 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2156 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2260715E-08 -6.2354797E-09 midg,1,midg; midg,igrid,midg 4.3510626E-09 -1.3885224E-09 1,midg,midg; igrid,midg,midg -1.1445928E-09 2.6423925E-09 gauss-seidel spectral radius is 0.9858206 estimated iterations to convergence 69 setup time was (sec) 0.6200000 now iterating at: 08:58:05 rms-change max change #iterations 9.4428830E-02 16.33586 at 10iterations 9.4119934E-03 1.702110 at 20iterations 2.0301593E-03 0.4095917 at 30iterations 7.5120881E-04 0.1565933 at 40iterations 2.9667022E-04 6.2023163E-02 at 50iterations finished qdiffx linear iterations at : 08:58:10 total time elapsed so far: 5.110000 # loops : 50 mean,max change (kT/e) : 2.9667022E-04 6.2023163E-02 energy calculations done at 5.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.270000 DelPhi exited at 08:58:10 5.276u 0.413s 0:06.01 94.5% 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 Wed Feb 15 2012 at 08:58:10 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 = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.813397 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): -18.12800 23.22900 ymin,ymax (A): -15.99700 32.48900 zmin,zma (A): 18.22900 77.12400 x,y,z range (A): 41.35700 48.48600 58.89500 scale (grids/A): 1.813397 object centre (A): 2.550500 8.246001 47.67650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000007 assigned positive charge : 313.9017 centred at (gu) : 89.31960 86.91930 86.48125 assigned negative charge : -311.9023 centred at (gu) : 89.14765 87.15216 87.26384 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 61375 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22215 grid for indexing accessible points = 1.400000 m= 20207 mr = 39529 m= 3014 mr = 13461 m= 140 mr = 1608 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 30103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17193 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) : 0.6044655 object centre at (A) : 2.550500 8.246001 47.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1398259E-02 -1.9692758E-02 midg,1,midg; midg,igrid,midg 2.8523589E-03 -1.2575913E-03 1,midg,midg; igrid,midg,midg -1.7279040E-03 6.5505053E-03 gauss-seidel spectral radius is 0.9984792 estimated iterations to convergence 203 setup time was (sec) 0.9000000 now iterating at: 08:58:11 rms-change max change #iterations 3.380941 184.2409 at 10iterations 1.510339 55.55882 at 20iterations 0.6759607 27.18674 at 30iterations 0.3028874 10.15213 at 40iterations 0.1365396 4.381626 at 50iterations 6.1628383E-02 2.175726 at 60iterations 2.7790003E-02 1.007906 at 70iterations 1.2947720E-02 0.5092354 at 80iterations 6.2970025E-03 0.2616310 at 90iterations 3.3191175E-03 0.1384659 at 100iterations 1.9783226E-03 8.6044312E-02 at 110iterations 1.3232266E-03 5.6629181E-02 at 120iterations finished qdiffx linear iterations at : 08:58:23 total time elapsed so far: 12.28000 # loops : 120 mean,max change (kT/e) : 1.3232266E-03 5.6629181E-02 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 08:58:23 12.439u 0.464s 0:13.34 96.6% 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 Wed Feb 15 2012 at 08:58:23 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 = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.720095 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): -18.12800 23.22900 ymin,ymax (A): -15.99700 32.48900 zmin,zma (A): 18.22900 77.12400 x,y,z range (A): 41.35700 48.48600 58.89500 scale (grids/A): 2.720095 object centre (A): 2.550500 8.246001 47.67650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000007 assigned positive charge : 313.9017 centred at (gu) : 88.97925 85.37876 84.72182 assigned negative charge : -311.9023 centred at (gu) : 88.72153 85.72829 85.89585 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 142258 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22215 grid for indexing accessible points = 1.400000 m= 65800 mr = 97455 m= 22809 mr = 50513 m= 4991 mr = 16981 m= 567 mr = 3344 m= 31 mr = 309 m= 0 mr = 9 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 67845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 17541 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) : 1.813397 object centre at (A) : 2.550500 8.246001 47.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6368283 -0.2474133 midg,1,midg; midg,igrid,midg 1.8394424E-02 -1.0314245E-02 1,midg,midg; igrid,midg,midg -2.7115667E-02 5.8662854E-02 gauss-seidel spectral radius is 0.9992180 estimated iterations to convergence 282 setup time was (sec) 1.700000 now iterating at: 08:58:26 rms-change max change #iterations 8.329057 339.4990 at 10iterations 4.824153 168.6708 at 20iterations 2.774201 58.47345 at 30iterations 1.591324 38.46650 at 40iterations 0.9087140 19.09028 at 50iterations 0.5176267 13.29497 at 60iterations 0.2946044 6.749367 at 70iterations 0.1679871 3.367035 at 80iterations 9.5401742E-02 1.895694 at 90iterations 5.4112636E-02 1.420701 at 100iterations 3.0695410E-02 0.7227516 at 110iterations 1.7436257E-02 0.3828862 at 120iterations 9.9711092E-03 0.2292023 at 130iterations 5.7288622E-03 0.1189766 at 140iterations 3.3391553E-03 7.8556061E-02 at 150iterations 2.0035943E-03 4.5837402E-02 at 160iterations 1.2687831E-03 2.9716492E-02 at 170iterations 8.6611632E-04 2.2869110E-02 at 180iterations finished qdiffx linear iterations at : 08:58:48 total time elapsed so far: 24.08000 # loops : 180 mean,max change (kT/e) : 8.6611632E-04 2.2869110E-02 energy calculations done at 24.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.24000 DelPhi exited at 08:58:49 24.247u 0.541s 0:25.35 97.7% 0+0k 0+0io 0pf+0w