Mon Oct 10 19:37:47 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 Mon Oct 10 2011 at 19:37:47 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 !!! WARNING: ASL 152 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5616825 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): -9.447001 40.28000 ymin,ymax (A): -9.684999 40.89100 zmin,zma (A): -0.8190000 62.56200 x,y,z range (A): 49.72700 50.57600 63.38100 scale (grids/A): 0.5616825 object centre (A): 15.41650 15.60300 30.87150 number of atom coordinates read : 2665 total number of charged atoms : 2528 net assigned charge : 4.400025 assigned positive charge : 393.2907 centred at (gu) : 90.44641 89.42234 89.32480 assigned negative charge : -388.8917 centred at (gu) : 90.34206 89.29075 89.33556 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5763 nv = 96 ne = 84 npr = 50982 no. pairs analyzed = 50982 no. exposed pairs = 3756 no. arc points = 26354 no. surface atoms = 1245 nbur = 1420 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 268 mr = 2878 m= 0 mr = 16 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2577 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7223 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1881284E-10 3.3496272E-10 midg,1,midg; midg,igrid,midg -1.0111139E-09 1.5951280E-09 1,midg,midg; igrid,midg,midg -5.2203986E-10 1.7398782E-09 gauss-seidel spectral radius is 0.9836361 estimated iterations to convergence 64 setup time was (sec) 0.6200000 now iterating at: 19:37:48 rms-change max change #iterations 7.9905041E-02 14.54368 at 10iterations 5.8027981E-03 1.056406 at 20iterations 4.3931059E-04 7.5078964E-02 at 30iterations 3.9428498E-05 6.0434341E-03 at 40iterations 5.5453670E-06 7.2669983E-04 at 50iterations finished qdiffx linear iterations at : 19:37:52 total time elapsed so far: 4.650000 # loops : 50 mean,max change (kT/e) : 5.5453670E-06 7.2669983E-04 energy calculations done at 4.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.820000 DelPhi exited at 19:37:53 4.823u 0.368s 0:05.70 90.8% 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 19:37:53 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 = 2665 !!! WARNING: ASL 152 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.685048 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): -9.447001 40.28000 ymin,ymax (A): -9.684999 40.89100 zmin,zma (A): -0.8190000 62.56200 x,y,z range (A): 49.72700 50.57600 63.38100 scale (grids/A): 1.685048 object centre (A): 15.41650 15.60300 30.87150 number of atom coordinates read : 2665 total number of charged atoms : 2528 net assigned charge : 4.400025 assigned positive charge : 393.2907 centred at (gu) : 91.33882 88.26660 87.97374 assigned negative charge : -388.8917 centred at (gu) : 91.02589 87.87207 88.00660 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63128 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26354 grid for indexing accessible points = 1.400000 m= 20212 mr = 41560 m= 2407 mr = 13788 m= 93 mr = 1244 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 172 time to turn everything in is 0.5200000 number of dielectric boundary points 29231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19521 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) : 0.5616825 object centre at (A) : 15.41650 15.60300 30.87150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3005569E-02 2.1833407E-02 midg,1,midg; midg,igrid,midg -8.3905095E-03 8.0553349E-03 1,midg,midg; igrid,midg,midg -4.6410956E-03 6.7878852E-04 gauss-seidel spectral radius is 0.9982864 estimated iterations to convergence 192 setup time was (sec) 0.8000000 now iterating at: 19:37:54 rms-change max change #iterations 3.343976 167.2156 at 10iterations 1.417818 57.90849 at 20iterations 0.6037030 21.25005 at 30iterations 0.2583482 10.38617 at 40iterations 0.1102815 4.507684 at 50iterations 4.7097668E-02 1.673444 at 60iterations 2.0098109E-02 0.7989883 at 70iterations 8.6191166E-03 0.3159300 at 80iterations 3.6765509E-03 0.1312237 at 90iterations 1.5743317E-03 5.3857803E-02 at 100iterations 6.7479810E-04 2.5302887E-02 at 110iterations 2.8868215E-04 1.0481834E-02 at 120iterations finished qdiffx linear iterations at : 19:38:04 total time elapsed so far: 10.47000 # loops : 120 mean,max change (kT/e) : 2.8868215E-04 1.0481834E-02 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.63000 DelPhi exited at 19:38:04 10.639u 0.459s 0:11.38 97.3% 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 19:38:04 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 !!! WARNING: ASL 152 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.527571 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): -9.447001 40.28000 ymin,ymax (A): -9.684999 40.89100 zmin,zma (A): -0.8190000 62.56200 x,y,z range (A): 49.72700 50.57600 63.38100 scale (grids/A): 2.527571 object centre (A): 15.41650 15.60300 30.87150 number of atom coordinates read : 2665 total number of charged atoms : 2528 net assigned charge : 4.400025 assigned positive charge : 393.2907 centred at (gu) : 92.00795 87.39956 86.96045 assigned negative charge : -388.8917 centred at (gu) : 91.53890 86.80808 87.00987 start vw surface at 0.1100000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 146271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26354 grid for indexing accessible points = 1.400000 m= 68150 mr = 101732 m= 20911 mr = 53356 m= 3925 mr = 15763 m= 335 mr = 2638 m= 7 mr = 159 m= 0 mr = 2 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 552 time to turn everything in is 1.290000 number of dielectric boundary points 65949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 20208 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) : 1.685048 object centre at (A) : 15.41650 15.60300 30.87150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2448578 0.4757040 midg,1,midg; midg,igrid,midg -8.4971093E-02 0.1147275 1,midg,midg; igrid,midg,midg -6.7136206E-02 -5.2674715E-03 gauss-seidel spectral radius is 0.9991764 estimated iterations to convergence 275 setup time was (sec) 1.610000 now iterating at: 19:38:06 rms-change max change #iterations 8.541293 333.3104 at 10iterations 4.896235 131.2180 at 20iterations 2.769191 67.83209 at 30iterations 1.564465 40.35731 at 40iterations 0.8810154 21.95199 at 50iterations 0.4942696 11.47470 at 60iterations 0.2766764 6.588329 at 70iterations 0.1547731 3.208080 at 80iterations 8.6369008E-02 1.826323 at 90iterations 4.8264690E-02 1.143341 at 100iterations 2.6904427E-02 0.5723233 at 110iterations 1.5014717E-02 0.3255463 at 120iterations 8.3855037E-03 0.1814423 at 130iterations 4.6631922E-03 9.7553253E-02 at 140iterations 2.5979241E-03 5.2631378E-02 at 150iterations 1.4454331E-03 2.8972626E-02 at 160iterations 8.0583751E-04 1.7520905E-02 at 170iterations 4.4796793E-04 8.8357925E-03 at 180iterations finished qdiffx linear iterations at : 19:38:24 total time elapsed so far: 18.88000 # loops : 180 mean,max change (kT/e) : 4.4796793E-04 8.8357925E-03 energy calculations done at 18.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.05000 DelPhi exited at 19:38:25 19.054u 0.465s 0:20.17 96.7% 0+0k 0+0io 0pf+0w