Sat Oct 8 13:17:40 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 Sat Oct 8 2011 at 13:17:40 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.6095786 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): 12.81600 64.88900 ymin,ymax (A): 1.299000 56.39600 zmin,zma (A): 87.92200 146.3230 x,y,z range (A): 52.07300 55.09700 58.40100 scale (grids/A): 0.6095786 object centre (A): 38.85250 28.84750 117.1225 number of atom coordinates read : 2976 total number of charged atoms : 2830 net assigned charge : -3.773961 assigned positive charge : 441.4388 centred at (gu) : 90.15108 92.75791 91.08353 assigned negative charge : -445.2140 centred at (gu) : 90.00999 92.70564 91.06754 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7419 nv = 96 ne = 84 npr = 60245 no. pairs analyzed = 60245 no. exposed pairs = 3766 no. arc points = 26035 no. surface atoms = 1264 nbur = 1712 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 361 mr = 4102 m= 0 mr = 37 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2200000 number of dielectric boundary points 3641 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2652 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9240 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5044362E-09 -1.7558630E-09 midg,1,midg; midg,igrid,midg -2.8408504E-09 1.2739068E-09 1,midg,midg; igrid,midg,midg -9.8998134E-09 5.6175886E-09 gauss-seidel spectral radius is 0.9860999 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 13:17:40 rms-change max change #iterations 0.1284894 22.61893 at 10iterations 1.1546203E-02 1.630814 at 20iterations 1.7297098E-03 0.2928066 at 30iterations 6.8041659E-04 0.1342373 at 40iterations 3.2597760E-04 6.5088272E-02 at 50iterations finished qdiffx linear iterations at : 13:17:43 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 3.2597760E-04 6.5088272E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 13:17:44 3.599u 0.192s 0:04.08 92.6% 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 Sat Oct 8 2011 at 13:17:44 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.828736 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): 12.81600 64.88900 ymin,ymax (A): 1.299000 56.39600 zmin,zma (A): 87.92200 146.3230 x,y,z range (A): 52.07300 55.09700 58.40100 scale (grids/A): 1.828736 object centre (A): 38.85250 28.84750 117.1225 number of atom coordinates read : 2976 total number of charged atoms : 2830 net assigned charge : -3.773961 assigned positive charge : 441.4388 centred at (gu) : 90.45212 98.27285 93.24950 assigned negative charge : -445.2140 centred at (gu) : 90.02959 98.11636 93.20258 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26035 grid for indexing accessible points = 1.400000 m= 28915 mr = 56247 m= 4129 mr = 21311 m= 188 mr = 2411 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 484 time to turn everything in is 0.4000000 number of dielectric boundary points 33706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 22138 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) : 0.6095786 object centre at (A) : 38.85250 28.84750 117.1225 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7881323E-02 -2.1925669E-02 midg,1,midg; midg,igrid,midg -1.6836667E-02 -9.4958907E-03 1,midg,midg; igrid,midg,midg -4.6668383E-03 -2.3409394E-03 gauss-seidel spectral radius is 0.9985588 estimated iterations to convergence 209 setup time was (sec) 0.6400000 now iterating at: 13:17:45 rms-change max change #iterations 4.225707 197.5039 at 10iterations 1.926724 60.69349 at 20iterations 0.8864678 27.10023 at 30iterations 0.4055067 12.50115 at 40iterations 0.1873397 6.109184 at 50iterations 8.5780084E-02 2.569345 at 60iterations 3.9494012E-02 1.247133 at 70iterations 1.8287167E-02 0.6210556 at 80iterations 8.6619295E-03 0.2529144 at 90iterations 4.2745308E-03 0.1373196 at 100iterations 2.3219197E-03 9.0524673E-02 at 110iterations 1.4424725E-03 6.0296059E-02 at 120iterations finished qdiffx linear iterations at : 13:17:52 total time elapsed so far: 8.330000 # loops : 120 mean,max change (kT/e) : 1.4424725E-03 6.0296059E-02 energy calculations done at 8.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 13:17:53 8.457u 0.247s 0:08.99 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 Sat Oct 8 2011 at 13:17:53 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.743104 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): 12.81600 64.88900 ymin,ymax (A): 1.299000 56.39600 zmin,zma (A): 87.92200 146.3230 x,y,z range (A): 52.07300 55.09700 58.40100 scale (grids/A): 2.743104 object centre (A): 38.85250 28.84750 117.1225 number of atom coordinates read : 2976 total number of charged atoms : 2830 net assigned charge : -3.773961 assigned positive charge : 441.4388 centred at (gu) : 90.67800 102.4090 94.87399 assigned negative charge : -445.2140 centred at (gu) : 90.04417 102.1743 94.80357 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 186191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26035 grid for indexing accessible points = 1.400000 m= 94586 mr = 136156 m= 32956 mr = 77558 m= 7163 mr = 26442 m= 807 mr = 5131 m= 34 mr = 442 m= 0 mr = 14 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1578 time to turn everything in is 1.060000 number of dielectric boundary points 75994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 22628 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) : 1.828736 object centre at (A) : 38.85250 28.84750 117.1225 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1687811 -0.3060794 midg,1,midg; midg,igrid,midg -0.3206133 -7.7749878E-02 1,midg,midg; igrid,midg,midg 2.0155463E-02 -0.1541312 gauss-seidel spectral radius is 0.9992493 estimated iterations to convergence 288 setup time was (sec) 1.350000 now iterating at: 13:17:54 rms-change max change #iterations 10.24330 310.6021 at 10iterations 6.021308 189.6258 at 20iterations 3.504395 75.48891 at 30iterations 2.036643 45.57005 at 40iterations 1.177692 24.32957 at 50iterations 0.6810547 13.99150 at 60iterations 0.3924383 7.619629 at 70iterations 0.2256344 4.463440 at 80iterations 0.1301295 2.586517 at 90iterations 7.4726336E-02 1.374174 at 100iterations 4.2974364E-02 0.7936144 at 110iterations 2.4695668E-02 0.5067539 at 120iterations 1.4232031E-02 0.2614632 at 130iterations 8.2782088E-03 0.1515465 at 140iterations 4.8662964E-03 9.5168114E-02 at 150iterations 2.9429006E-03 6.1048508E-02 at 160iterations 1.8668728E-03 4.2251587E-02 at 170iterations 1.2773086E-03 3.1257629E-02 at 180iterations finished qdiffx linear iterations at : 13:18:08 total time elapsed so far: 14.46000 # loops : 180 mean,max change (kT/e) : 1.2773086E-03 3.1257629E-02 energy calculations done at 14.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.59000 DelPhi exited at 13:18:08 14.591u 0.277s 0:15.15 98.0% 0+0k 0+0io 0pf+0w