Tue Oct 11 06:01:54 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 Tue Oct 11 2011 at 06:01:54 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2268 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7348388 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): 25.60200 71.89600 ymin,ymax (A): -18.58900 29.85700 zmin,zma (A): 4.176000 46.23300 x,y,z range (A): 46.29400 48.44600 42.05700 scale (grids/A): 0.7348388 object centre (A): 48.74900 5.634001 25.20450 number of atom coordinates read : 2268 total number of charged atoms : 1943 net assigned charge : 5.945010 assigned positive charge : 315.5760 centred at (gu) : 89.22909 90.40333 90.20632 assigned negative charge : -309.6312 centred at (gu) : 89.35943 90.33264 90.28033 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7732 nv = 96 ne = 84 npr = 41308 no. pairs analyzed = 41308 no. exposed pairs = 2565 no. arc points = 17431 no. surface atoms = 879 nbur = 1389 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 591 mr = 4534 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3669 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1521 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8208 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5161528E-07 2.7557769E-08 midg,1,midg; midg,igrid,midg 2.7884724E-08 1.6672983E-07 1,midg,midg; igrid,midg,midg 2.3866946E-07 -2.0007427E-08 gauss-seidel spectral radius is 0.9903407 estimated iterations to convergence 83 setup time was (sec) 0.5300000 now iterating at: 06:01:55 rms-change max change #iterations 0.2368174 36.59964 at 10iterations 3.1892613E-02 4.087249 at 20iterations 4.6345228E-03 0.5562449 at 30iterations 8.3094981E-04 0.1042366 at 40iterations 2.2587388E-04 2.9407501E-02 at 50iterations finished qdiffx linear iterations at : 06:01:58 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.2587388E-04 2.9407501E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:01:58 3.335u 0.178s 0:04.05 86.4% 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 06:01:58 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2268 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.204516 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): 25.60200 71.89600 ymin,ymax (A): -18.58900 29.85700 zmin,zma (A): 4.176000 46.23300 x,y,z range (A): 46.29400 48.44600 42.05700 scale (grids/A): 2.204516 object centre (A): 48.74900 5.634001 25.20450 number of atom coordinates read : 2268 total number of charged atoms : 1943 net assigned charge : 5.945010 assigned positive charge : 315.5760 centred at (gu) : 87.68736 91.20990 90.61885 assigned negative charge : -309.6312 centred at (gu) : 88.07854 90.99808 90.84112 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17431 grid for indexing accessible points = 1.400000 m= 34369 mr = 58503 m= 7386 mr = 26505 m= 791 mr = 5169 m= 27 mr = 407 m= 0 mr = 7 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 33490 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15457 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) : 0.7348388 object centre at (A) : 48.74900 5.634001 25.20450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2778044E-02 3.2319389E-02 midg,1,midg; midg,igrid,midg 4.7217712E-02 3.4884233E-02 1,midg,midg; igrid,midg,midg 4.6089984E-02 -5.7809271E-02 gauss-seidel spectral radius is 0.9989052 estimated iterations to convergence 239 setup time was (sec) 0.8900000 now iterating at: 06:02:00 rms-change max change #iterations 4.936687 183.5322 at 10iterations 2.497425 82.84175 at 20iterations 1.271355 37.23651 at 30iterations 0.6458231 18.22800 at 40iterations 0.3269133 9.415907 at 50iterations 0.1666200 4.536053 at 60iterations 8.4724434E-02 2.359131 at 70iterations 4.3169841E-02 1.119862 at 80iterations 2.2108346E-02 0.6234329 at 90iterations 1.1375163E-02 0.3061790 at 100iterations 5.9083244E-03 0.1786203 at 110iterations 3.1225125E-03 9.7770691E-02 at 120iterations finished qdiffx linear iterations at : 06:02:06 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 3.1225125E-03 9.7770691E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 06:02:08 7.598u 0.230s 0:09.52 82.1% 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 Tue Oct 11 2011 at 06:02:08 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2268 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.306775 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): 25.60200 71.89600 ymin,ymax (A): -18.58900 29.85700 zmin,zma (A): 4.176000 46.23300 x,y,z range (A): 46.29400 48.44600 42.05700 scale (grids/A): 3.306775 object centre (A): 48.74900 5.634001 25.20450 number of atom coordinates read : 2268 total number of charged atoms : 1943 net assigned charge : 5.945010 assigned positive charge : 315.5760 centred at (gu) : 86.53111 91.81493 90.92824 assigned negative charge : -309.6312 centred at (gu) : 87.11785 91.49704 91.26162 start vw surface at 0.1900000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 187703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17431 grid for indexing accessible points = 1.400000 m= 104907 mr = 140478 m= 45199 mr = 88022 m= 14291 mr = 37769 m= 3164 mr = 11340 m= 428 mr = 2337 m= 27 mr = 305 m= 0 mr = 4 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.020000 number of dielectric boundary points 75464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 15544 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) : 2.204516 object centre at (A) : 48.74900 5.634001 25.20450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2712045E-02 0.2716092 midg,1,midg; midg,igrid,midg 0.3138111 0.1797338 1,midg,midg; igrid,midg,midg 0.4461984 -0.6839117 gauss-seidel spectral radius is 0.9993153 estimated iterations to convergence 301 setup time was (sec) 2.340000 now iterating at: 06:02:11 rms-change max change #iterations 10.72844 344.2871 at 10iterations 6.389748 123.8837 at 20iterations 3.800496 73.78776 at 30iterations 2.263707 41.57517 at 40iterations 1.341243 24.08104 at 50iterations 0.7937593 13.22905 at 60iterations 0.4694980 8.349585 at 70iterations 0.2780060 4.900139 at 80iterations 0.1642118 3.184654 at 90iterations 9.7140983E-02 1.659164 at 100iterations 5.7570182E-02 1.043552 at 110iterations 3.4396768E-02 0.5768242 at 120iterations 2.0675121E-02 0.4043961 at 130iterations 1.2693892E-02 0.2418633 at 140iterations 8.0518918E-03 0.1479912 at 150iterations 5.3647086E-03 0.1025047 at 160iterations 3.7620484E-03 7.4745178E-02 at 170iterations 2.8039750E-03 4.9545288E-02 at 180iterations finished qdiffx linear iterations at : 06:02:21 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 2.8039750E-03 4.9545288E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 06:02:22 13.191u 0.244s 0:14.33 93.7% 0+0k 0+0io 0pf+0w