Sat Oct 8 11:43:06 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 11:43:06 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 = 4565 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5539563 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): -27.08400 35.11900 ymin,ymax (A): 34.95600 99.22100 zmin,zma (A): 31.12300 89.28100 x,y,z range (A): 62.20300 64.26500 58.15800 scale (grids/A): 0.5539563 object centre (A): 4.017500 67.08850 60.20200 number of atom coordinates read : 4565 total number of charged atoms : 4404 net assigned charge : -5.499951 assigned positive charge : 689.2216 centred at (gu) : 90.85107 87.95123 89.05924 assigned negative charge : -694.7253 centred at (gu) : 90.71148 88.04105 89.24934 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8814 nv = 96 ne = 84 npr = 96230 no. pairs analyzed = 96230 no. exposed pairs = 5101 no. arc points = 34877 no. surface atoms = 1722 nbur = 2843 mkacc time = 0.2100000 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= 364 mr = 5124 m= 0 mr = 23 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 144 time to turn everything in is 0.4300000 number of dielectric boundary points 4031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3587 ## 450 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11815 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5858551E-09 -2.5634850E-09 midg,1,midg; midg,igrid,midg 1.1869092E-09 -1.0898911E-09 1,midg,midg; igrid,midg,midg -2.0297770E-09 1.6971171E-09 gauss-seidel spectral radius is 0.9833018 estimated iterations to convergence 64 setup time was (sec) 0.7400000 now iterating at: 11:43:07 rms-change max change #iterations 9.9829905E-02 13.99566 at 10iterations 7.3108026E-03 0.9371948 at 20iterations 7.7645108E-04 0.1030121 at 30iterations 1.6948403E-04 2.1800518E-02 at 40iterations 5.3117794E-05 7.3068142E-03 at 50iterations finished qdiffx linear iterations at : 11:43:11 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 5.3117794E-05 7.3068142E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 11:43:12 4.510u 0.284s 0:05.07 94.4% 0+0k 0+0io 6pf+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 11:43:12 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 = 4565 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.661869 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): -27.08400 35.11900 ymin,ymax (A): 34.95600 99.22100 zmin,zma (A): 31.12300 89.28100 x,y,z range (A): 62.20300 64.26500 58.15800 scale (grids/A): 1.661869 object centre (A): 4.017500 67.08850 60.20200 number of atom coordinates read : 4565 total number of charged atoms : 4404 net assigned charge : -5.499951 assigned positive charge : 689.2216 centred at (gu) : 92.55168 83.85232 87.17647 assigned negative charge : -694.7253 centred at (gu) : 92.13386 84.12267 87.74764 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 99643 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34877 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 32254 mr = 72397 m= 3776 mr = 23746 m= 101 mr = 2254 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 5898 time to turn everything in is 0.7100000 number of dielectric boundary points 37353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 381 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 33897 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) : 0.5539563 object centre at (A) : 4.017500 67.08850 60.20200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7881337E-02 -2.3080254E-02 midg,1,midg; midg,igrid,midg 2.2386402E-02 -3.4071822E-03 1,midg,midg; igrid,midg,midg -2.7269749E-02 2.2296224E-02 gauss-seidel spectral radius is 0.9983832 estimated iterations to convergence 197 setup time was (sec) 1.040000 now iterating at: 11:43:13 rms-change max change #iterations 4.428814 161.1593 at 10iterations 1.935831 64.29187 at 20iterations 0.8532969 24.04258 at 30iterations 0.3749479 10.95845 at 40iterations 0.1642374 4.791416 at 50iterations 7.2125599E-02 2.125396 at 60iterations 3.1795792E-02 0.8619103 at 70iterations 1.3955741E-02 0.4295273 at 80iterations 6.1745699E-03 0.1838036 at 90iterations 2.7354863E-03 8.0276489E-02 at 100iterations 1.2306973E-03 3.3646584E-02 at 110iterations 5.6770397E-04 1.8402576E-02 at 120iterations finished qdiffx linear iterations at : 11:43:22 total time elapsed so far: 9.720000 # loops : 120 mean,max change (kT/e) : 5.6770397E-04 1.8402576E-02 energy calculations done at 9.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.910000 DelPhi exited at 11:43:22 9.912u 0.258s 0:10.44 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 Sat Oct 8 2011 at 11:43:22 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 = 4565 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.492803 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): -27.08400 35.11900 ymin,ymax (A): 34.95600 99.22100 zmin,zma (A): 31.12300 89.28100 x,y,z range (A): 62.20300 64.26500 58.15800 scale (grids/A): 2.492803 object centre (A): 4.017500 67.08850 60.20200 number of atom coordinates read : 4565 total number of charged atoms : 4404 net assigned charge : -5.499951 assigned positive charge : 689.2216 centred at (gu) : 93.82714 80.77821 85.76428 assigned negative charge : -694.7253 centred at (gu) : 93.20056 81.18388 86.62128 start vw surface at 0.1800000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 231876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34877 grid for indexing accessible points = 1.400000 m= 111883 mr = 175862 m= 33530 mr = 92306 m= 6317 mr = 26612 m= 555 mr = 4739 m= 10 mr = 322 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 19424 time to turn everything in is 1.770000 number of dielectric boundary points 84330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 35207 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) : 1.661869 object centre at (A) : 4.017500 67.08850 60.20200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4831053 -0.2891106 midg,1,midg; midg,igrid,midg 0.3957669 0.1197642 1,midg,midg; igrid,midg,midg -0.3669256 0.2765636 gauss-seidel spectral radius is 0.9992156 estimated iterations to convergence 282 setup time was (sec) 2.110000 now iterating at: 11:43:24 rms-change max change #iterations 11.07991 360.4631 at 10iterations 6.357079 119.1712 at 20iterations 3.641230 71.29159 at 30iterations 2.080692 41.09002 at 40iterations 1.182888 20.44988 at 50iterations 0.6721433 10.95906 at 60iterations 0.3825189 6.111712 at 70iterations 0.2171320 3.770616 at 80iterations 0.1230228 2.104962 at 90iterations 6.9783159E-02 1.242640 at 100iterations 3.9529454E-02 0.6685638 at 110iterations 2.2364765E-02 0.3929157 at 120iterations 1.2705709E-02 0.2182655 at 130iterations 7.1993261E-03 0.1322410 at 140iterations 4.0967828E-03 6.5056801E-02 at 150iterations 2.3405356E-03 4.0473938E-02 at 160iterations 1.3423662E-03 2.1789551E-02 at 170iterations 7.8214234E-04 1.3753891E-02 at 180iterations finished qdiffx linear iterations at : 11:43:39 total time elapsed so far: 16.27000 # loops : 180 mean,max change (kT/e) : 7.8214234E-04 1.3753891E-02 energy calculations done at 16.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.44000 DelPhi exited at 11:43:39 16.445u 0.298s 0:17.01 98.3% 0+0k 0+0io 0pf+0w