Sat Oct 15 12:15:03 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 Sat Oct 15 2011 at 12:15:03 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: HIT 81 has a net charge of 0.5140 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: 0.5572687 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): -20.93300 31.73200 ymin,ymax (A): 57.43600 118.0560 zmin,zma (A): -3.9000034E-02 63.84400 x,y,z range (A): 52.66500 60.62000 63.88300 scale (grids/A): 0.5572687 object centre (A): 5.399500 87.74600 31.90250 number of atom coordinates read : 3208 total number of charged atoms : 3067 net assigned charge : 14.51403 assigned positive charge : 475.6297 centred at (gu) : 90.10150 89.16405 89.52585 assigned negative charge : -461.1174 centred at (gu) : 90.22344 89.07586 89.33247 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6877 nv = 96 ne = 84 npr = 61370 no. pairs analyzed = 61370 no. exposed pairs = 4430 no. arc points = 32069 no. surface atoms = 1466 nbur = 1742 mkacc time = 0.1600000 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= 295 mr = 3396 m= 0 mr = 8 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3236 ## 413 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8771 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3567252E-10 3.0179279E-09 midg,1,midg; midg,igrid,midg 5.8431809E-10 1.9047348E-09 1,midg,midg; igrid,midg,midg 2.6039724E-09 1.2927845E-10 gauss-seidel spectral radius is 0.9834267 estimated iterations to convergence 64 setup time was (sec) 0.6900000 now iterating at: 12:15:04 rms-change max change #iterations 8.3439142E-02 13.63910 at 10iterations 5.9577147E-03 0.8860474 at 20iterations 4.6152709E-04 7.6032639E-02 at 30iterations 6.2825253E-05 1.3853550E-02 at 40iterations 1.5263846E-05 3.9281845E-03 at 50iterations finished qdiffx linear iterations at : 12:15:12 total time elapsed so far: 5.440000 # loops : 50 mean,max change (kT/e) : 1.5263846E-05 3.9281845E-03 energy calculations done at 5.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.610000 DelPhi exited at 12:15:13 5.615u 0.445s 0:09.43 64.1% 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 Sat Oct 15 2011 at 12:15:13 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: HIT 81 has a net charge of 0.5140 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: 1.671806 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): -20.93300 31.73200 ymin,ymax (A): 57.43600 118.0560 zmin,zma (A): -3.9000034E-02 63.84400 x,y,z range (A): 52.66500 60.62000 63.88300 scale (grids/A): 1.671806 object centre (A): 5.399500 87.74600 31.90250 number of atom coordinates read : 3208 total number of charged atoms : 3067 net assigned charge : 14.51403 assigned positive charge : 475.6297 centred at (gu) : 90.30327 87.49091 88.57694 assigned negative charge : -461.1174 centred at (gu) : 90.67028 87.22739 87.99747 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32069 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24016 mr = 49376 m= 2720 mr = 16350 m= 61 mr = 1255 m= 0 mr = 4 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 195 time to turn everything in is 0.6500000 number of dielectric boundary points 35037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 23603 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) : 0.5572687 object centre at (A) : 5.399500 87.74600 31.90250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2477187E-02 7.1710697E-03 midg,1,midg; midg,igrid,midg 1.6109101E-03 2.0159580E-02 1,midg,midg; igrid,midg,midg 4.3374613E-02 1.3129829E-02 gauss-seidel spectral radius is 0.9983198 estimated iterations to convergence 194 setup time was (sec) 1.000000 now iterating at: 12:15:15 rms-change max change #iterations 3.596385 171.1346 at 10iterations 1.540094 63.33456 at 20iterations 0.6611545 23.32913 at 30iterations 0.2849820 10.60164 at 40iterations 0.1228616 4.380899 at 50iterations 5.2707884E-02 1.847672 at 60iterations 2.2661109E-02 0.8121787 at 70iterations 9.7456109E-03 0.3224792 at 80iterations 4.2145397E-03 0.1434975 at 90iterations 1.8176669E-03 6.0979843E-02 at 100iterations 7.8759139E-04 2.6513815E-02 at 110iterations 3.4114195E-04 1.1777401E-02 at 120iterations finished qdiffx linear iterations at : 12:15:29 total time elapsed so far: 13.12000 # loops : 120 mean,max change (kT/e) : 3.4114195E-04 1.1777401E-02 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.30000 DelPhi exited at 12:15:30 13.309u 0.514s 0:16.79 82.2% 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 Sat Oct 15 2011 at 12:15:30 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: HIT 81 has a net charge of 0.5140 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: 2.507709 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): -20.93300 31.73200 ymin,ymax (A): 57.43600 118.0560 zmin,zma (A): -3.9000034E-02 63.84400 x,y,z range (A): 52.66500 60.62000 63.88300 scale (grids/A): 2.507709 object centre (A): 5.399500 87.74600 31.90250 number of atom coordinates read : 3208 total number of charged atoms : 3067 net assigned charge : 14.51403 assigned positive charge : 475.6297 centred at (gu) : 90.45466 86.23604 87.86523 assigned negative charge : -461.1174 centred at (gu) : 91.00526 85.84097 86.99607 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 174625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32069 grid for indexing accessible points = 1.400000 m= 81025 mr = 121262 m= 24733 mr = 63235 m= 4277 mr = 18389 m= 324 mr = 2724 m= 3 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.9800001 no. cavity mid-points inaccessible to solvent = 736 time to turn everything in is 1.620000 number of dielectric boundary points 79264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 24511 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) : 1.671806 object centre at (A) : 5.399500 87.74600 31.90250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2895077 -0.2797511 midg,1,midg; midg,igrid,midg 5.8566727E-02 0.3383404 1,midg,midg; igrid,midg,midg 0.6687066 0.1773132 gauss-seidel spectral radius is 0.9991947 estimated iterations to convergence 278 setup time was (sec) 2.010000 now iterating at: 12:15:32 rms-change max change #iterations 9.278050 317.6439 at 10iterations 5.361083 135.6156 at 20iterations 3.067245 63.27571 at 30iterations 1.750127 34.96084 at 40iterations 0.9933752 21.28501 at 50iterations 0.5626309 12.94125 at 60iterations 0.3177238 6.478518 at 70iterations 0.1792841 4.203611 at 80iterations 0.1007478 1.945200 at 90iterations 5.6651611E-02 1.056305 at 100iterations 3.1888578E-02 0.5955963 at 110iterations 1.7907409E-02 0.3563430 at 120iterations 1.0062800E-02 0.2103004 at 130iterations 5.6394171E-03 0.1042061 at 140iterations 3.1643503E-03 5.9641838E-02 at 150iterations 1.7744277E-03 3.4399033E-02 at 160iterations 9.9684845E-04 1.7448425E-02 at 170iterations 5.5935199E-04 1.0657310E-02 at 180iterations finished qdiffx linear iterations at : 12:15:52 total time elapsed so far: 21.83000 # loops : 180 mean,max change (kT/e) : 5.5935199E-04 1.0657310E-02 energy calculations done at 21.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.01000 DelPhi exited at 12:15:53 22.011u 0.540s 0:22.95 98.2% 0+0k 0+0io 0pf+0w