Tue Oct 11 08:33:13 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 08:33:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2130 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7163410 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): -19.85000 26.48400 ymin,ymax (A): -12.10300 28.45900 zmin,zma (A): -2.698000 46.99900 x,y,z range (A): 46.33400 40.56200 49.69700 scale (grids/A): 0.7163410 object centre (A): 3.317000 8.177999 22.15050 number of atom coordinates read : 2130 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 89.41441 89.59454 90.67229 assigned negative charge : -318.8441 centred at (gu) : 89.27826 89.60891 90.75513 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7411 nv = 96 ne = 84 npr = 42949 no. pairs analyzed = 42949 no. exposed pairs = 2544 no. arc points = 17117 no. surface atoms = 869 nbur = 1261 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 510 mr = 4369 m= 4 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1614 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 8156 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0466062E-07 1.8967130E-08 midg,1,midg; midg,igrid,midg 8.3370928E-08 5.5334070E-08 1,midg,midg; igrid,midg,midg -1.8879373E-08 1.3496373E-07 gauss-seidel spectral radius is 0.9898412 estimated iterations to convergence 81 setup time was (sec) 0.3400000 now iterating at: 08:33:13 rms-change max change #iterations 0.2152763 30.61998 at 10iterations 2.7251495E-02 3.658447 at 20iterations 3.5414968E-03 0.4564333 at 30iterations 4.8865529E-04 6.3014984E-02 at 40iterations 8.4724255E-05 1.2107849E-02 at 50iterations finished qdiffx linear iterations at : 08:33:16 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 8.4724255E-05 1.2107849E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 08:33:17 3.322u 0.185s 0:04.07 85.9% 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 08:33:17 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 = 2130 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.149023 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): -19.85000 26.48400 ymin,ymax (A): -12.10300 28.45900 zmin,zma (A): -2.698000 46.99900 x,y,z range (A): 46.33400 40.56200 49.69700 scale (grids/A): 2.149023 object centre (A): 3.317000 8.177999 22.15050 number of atom coordinates read : 2130 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 88.24327 88.78363 92.01659 assigned negative charge : -318.8441 centred at (gu) : 87.83498 88.82672 92.26525 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17117 grid for indexing accessible points = 1.400000 m= 31705 mr = 55804 m= 6430 mr = 24318 m= 592 mr = 4332 m= 19 mr = 284 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 31920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15904 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) : 0.7163410 object centre at (A) : 3.317000 8.177999 22.15050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2634081E-02 6.6299118E-02 midg,1,midg; midg,igrid,midg 3.1339057E-02 5.0843004E-03 1,midg,midg; igrid,midg,midg 9.3527092E-03 3.7567027E-02 gauss-seidel spectral radius is 0.9988574 estimated iterations to convergence 234 setup time was (sec) 0.6300000 now iterating at: 08:33:18 rms-change max change #iterations 4.765557 166.8885 at 10iterations 2.379302 77.90192 at 20iterations 1.198112 35.25301 at 30iterations 0.5939369 16.87242 at 40iterations 0.2996287 8.975435 at 50iterations 0.1497293 4.362875 at 60iterations 7.5259775E-02 2.198303 at 70iterations 3.7627496E-02 1.123619 at 80iterations 1.8870572E-02 0.5490952 at 90iterations 9.4711017E-03 0.2730117 at 100iterations 4.7573112E-03 0.1573057 at 110iterations 2.4107748E-03 6.9271088E-02 at 120iterations finished qdiffx linear iterations at : 08:33:25 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 2.4107748E-03 6.9271088E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 08:33:25 7.870u 0.183s 0:08.53 94.3% 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 Tue Oct 11 2011 at 08:33:25 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 = 2130 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.223535 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): -19.85000 26.48400 ymin,ymax (A): -12.10300 28.45900 zmin,zma (A): -2.698000 46.99900 x,y,z range (A): 46.33400 40.56200 49.69700 scale (grids/A): 3.223535 object centre (A): 3.317000 8.177999 22.15050 number of atom coordinates read : 2130 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 87.36494 88.17545 93.02486 assigned negative charge : -318.8441 centred at (gu) : 86.75250 88.24001 93.39781 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 179584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17117 grid for indexing accessible points = 1.400000 m= 98383 mr = 133990 m= 40814 mr = 82313 m= 12096 mr = 33912 m= 2377 mr = 9397 m= 254 mr = 1672 m= 3 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 72093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 16012 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) : 2.149023 object centre at (A) : 3.317000 8.177999 22.15050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3950808 0.7957274 midg,1,midg; midg,igrid,midg 0.2341980 -8.0896569E-03 1,midg,midg; igrid,midg,midg 0.2560834 0.3306129 gauss-seidel spectral radius is 0.9993017 estimated iterations to convergence 299 setup time was (sec) 1.410000 now iterating at: 08:33:27 rms-change max change #iterations 10.53635 463.6858 at 10iterations 6.256567 129.3609 at 20iterations 3.697721 66.26432 at 30iterations 2.184472 40.52673 at 40iterations 1.287823 22.80766 at 50iterations 0.7563075 12.84624 at 60iterations 0.4456084 7.316261 at 70iterations 0.2615989 4.259033 at 80iterations 0.1534474 2.884655 at 90iterations 9.0106331E-02 1.534718 at 100iterations 5.2961685E-02 0.8869123 at 110iterations 3.1235255E-02 0.5058899 at 120iterations 1.8423494E-02 0.3123915 at 130iterations 1.0984328E-02 0.1923065 at 140iterations 6.6254302E-03 0.1191301 at 150iterations 4.0710149E-03 7.2128296E-02 at 160iterations 2.5958696E-03 4.5562744E-02 at 170iterations 1.7389461E-03 3.5770416E-02 at 180iterations finished qdiffx linear iterations at : 08:33:38 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 1.7389461E-03 3.5770416E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 08:33:39 12.793u 0.226s 0:13.63 95.4% 0+0k 0+0io 0pf+0w