Tue Oct 11 08:35:43 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 Tue Oct 11 2011 at 08:35:43 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2336 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: 0.6501214 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): -12.55300 36.93500 ymin,ymax (A): -27.32800 16.24600 zmin,zma (A): -9.229000 45.53000 x,y,z range (A): 49.48800 43.57400 54.75900 scale (grids/A): 0.6501214 object centre (A): 12.19100 -5.540999 18.15050 number of atom coordinates read : 2336 total number of charged atoms : 2230 net assigned charge : 2.000011 assigned positive charge : 355.6061 centred at (gu) : 90.36716 90.70484 91.95138 assigned negative charge : -353.6068 centred at (gu) : 90.12141 90.55621 91.93846 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6816 nv = 96 ne = 84 npr = 45170 no. pairs analyzed = 45170 no. exposed pairs = 3046 no. arc points = 21303 no. surface atoms = 1017 nbur = 1319 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3753 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2063 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8070 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2355700E-09 8.0778122E-09 midg,1,midg; midg,igrid,midg -1.4923138E-08 2.7780612E-08 1,midg,midg; igrid,midg,midg -2.9054940E-08 3.9824375E-08 gauss-seidel spectral radius is 0.9877197 estimated iterations to convergence 74 setup time was (sec) 0.4900000 now iterating at: 08:35:44 rms-change max change #iterations 0.1489933 19.94220 at 10iterations 1.5297598E-02 2.411239 at 20iterations 1.6221009E-03 0.2245536 at 30iterations 1.9635668E-04 2.7894974E-02 at 40iterations 2.9122770E-05 3.8070679E-03 at 50iterations finished qdiffx linear iterations at : 08:35:46 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 2.9122770E-05 3.8070679E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 08:35:47 3.081u 0.146s 0:03.76 85.6% 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 Tue Oct 11 2011 at 08:35:47 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2336 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: 1.950364 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): -12.55300 36.93500 ymin,ymax (A): -27.32800 16.24600 zmin,zma (A): -9.229000 45.53000 x,y,z range (A): 49.48800 43.57400 54.75900 scale (grids/A): 1.950364 object centre (A): 12.19100 -5.540999 18.15050 number of atom coordinates read : 2336 total number of charged atoms : 2230 net assigned charge : 2.000011 assigned positive charge : 355.6061 centred at (gu) : 91.10093 92.11401 95.85365 assigned negative charge : -353.6068 centred at (gu) : 90.36430 91.66856 95.81525 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72341 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21303 grid for indexing accessible points = 1.400000 m= 28056 mr = 49855 m= 4907 mr = 20951 m= 318 mr = 3041 m= 3 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 31658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 17583 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) : 0.6501214 object centre at (A) : 12.19100 -5.540999 18.15050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7494262E-03 -2.6686343E-03 midg,1,midg; midg,igrid,midg -9.3299579E-03 1.3006356E-02 1,midg,midg; igrid,midg,midg -1.2372911E-02 4.9008261E-02 gauss-seidel spectral radius is 0.9986755 estimated iterations to convergence 218 setup time was (sec) 0.7900000 now iterating at: 08:35:48 rms-change max change #iterations 4.213984 183.7491 at 10iterations 2.002660 73.12711 at 20iterations 0.9523274 29.25367 at 30iterations 0.4513518 14.50942 at 40iterations 0.2145262 7.115366 at 50iterations 0.1012966 3.473896 at 60iterations 4.7966145E-02 1.486503 at 70iterations 2.2854693E-02 0.7394479 at 80iterations 1.0860976E-02 0.3538876 at 90iterations 5.1497249E-03 0.1654048 at 100iterations 2.4539791E-03 7.9154491E-02 at 110iterations 1.1795571E-03 3.6104918E-02 at 120iterations finished qdiffx linear iterations at : 08:35:54 total time elapsed so far: 6.760000 # loops : 120 mean,max change (kT/e) : 1.1795571E-03 3.6104918E-02 energy calculations done at 6.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 08:35:54 6.928u 0.159s 0:07.43 95.1% 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 Tue Oct 11 2011 at 08:35:54 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2336 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: 2.925546 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): -12.55300 36.93500 ymin,ymax (A): -27.32800 16.24600 zmin,zma (A): -9.229000 45.53000 x,y,z range (A): 49.48800 43.57400 54.75900 scale (grids/A): 2.925546 object centre (A): 12.19100 -5.540999 18.15050 number of atom coordinates read : 2336 total number of charged atoms : 2230 net assigned charge : 2.000011 assigned positive charge : 355.6061 centred at (gu) : 91.65130 93.17084 98.78032 assigned negative charge : -353.6068 centred at (gu) : 90.54639 92.50279 98.72283 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 166705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21303 grid for indexing accessible points = 1.400000 m= 88359 mr = 120484 m= 34437 mr = 72470 m= 8879 mr = 27862 m= 1402 mr = 6623 m= 84 mr = 927 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 71464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 17840 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) : 1.950364 object centre at (A) : 12.19100 -5.540999 18.15050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4391154E-02 8.9221023E-02 midg,1,midg; midg,igrid,midg -9.8153934E-02 7.9994008E-02 1,midg,midg; igrid,midg,midg -0.1077110 0.4396636 gauss-seidel spectral radius is 0.9992637 estimated iterations to convergence 291 setup time was (sec) 1.600000 now iterating at: 08:35:56 rms-change max change #iterations 9.812715 347.6265 at 10iterations 5.720571 136.8661 at 20iterations 3.327334 82.18279 at 30iterations 1.929910 39.29229 at 40iterations 1.117897 22.88947 at 50iterations 0.6473279 13.15483 at 60iterations 0.3738000 6.996338 at 70iterations 0.2157430 4.011025 at 80iterations 0.1241586 2.240925 at 90iterations 7.1766913E-02 1.318308 at 100iterations 4.1365482E-02 0.7747307 at 110iterations 2.3900695E-02 0.5125313 at 120iterations 1.3793823E-02 0.2621899 at 130iterations 7.9475837E-03 0.1389065 at 140iterations 4.6175178E-03 8.1520081E-02 at 150iterations 2.6883099E-03 4.6905518E-02 at 160iterations 1.5797428E-03 2.9747009E-02 at 170iterations 9.4380783E-04 1.7486572E-02 at 180iterations finished qdiffx linear iterations at : 08:36:06 total time elapsed so far: 11.09000 # loops : 180 mean,max change (kT/e) : 9.4380783E-04 1.7486572E-02 energy calculations done at 11.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 08:36:06 11.285u 0.224s 0:12.04 95.5% 0+0k 0+0io 0pf+0w