Mon Oct 10 16:11:58 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 Mon Oct 10 2011 at 16:11:58 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 = 3636 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 has a net charge of 1.4000 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: 0.5735737 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): -17.72100 31.47000 ymin,ymax (A): -32.40300 29.66400 zmin,zma (A): -25.90100 35.62400 x,y,z range (A): 49.19100 62.06700 61.52500 scale (grids/A): 0.5735737 object centre (A): 6.874499 -1.369500 4.861501 number of atom coordinates read : 3636 total number of charged atoms : 3531 net assigned charge : 4.700007 assigned positive charge : 540.6578 centred at (gu) : 90.73504 89.86468 88.68902 assigned negative charge : -535.9601 centred at (gu) : 90.79440 89.93150 88.62321 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8110 nv = 96 ne = 84 npr = 72609 no. pairs analyzed = 72609 no. exposed pairs = 4702 no. arc points = 32472 no. surface atoms = 1592 nbur = 2044 mkacc time = 0.1800000 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 = 1.484000 m= 425 mr = 4373 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.4100000 number of dielectric boundary points 4121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3288 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10389 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.9923079E-10 1.6478086E-09 midg,1,midg; midg,igrid,midg 2.3364566E-09 -5.7040056E-10 1,midg,midg; igrid,midg,midg 1.7714499E-09 -5.2073401E-10 gauss-seidel spectral radius is 0.9843737 estimated iterations to convergence 66 setup time was (sec) 0.6900000 now iterating at: 16:12:00 rms-change max change #iterations 0.1072328 15.41045 at 10iterations 8.1969919E-03 1.353110 at 20iterations 7.0406281E-04 0.1020126 at 30iterations 1.0950337E-04 1.4888763E-02 at 40iterations 3.1355274E-05 4.4307709E-03 at 50iterations finished qdiffx linear iterations at : 16:12:03 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 3.1355274E-05 4.4307709E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 16:12:04 4.653u 0.375s 0:05.30 94.7% 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 Mon Oct 10 2011 at 16:12:04 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 = 3636 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 has a net charge of 1.4000 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: 1.720721 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): -17.72100 31.47000 ymin,ymax (A): -32.40300 29.66400 zmin,zma (A): -25.90100 35.62400 x,y,z range (A): 49.19100 62.06700 61.52500 scale (grids/A): 1.720721 object centre (A): 6.874499 -1.369500 4.861501 number of atom coordinates read : 3636 total number of charged atoms : 3531 net assigned charge : 4.700007 assigned positive charge : 540.6578 centred at (gu) : 92.20415 89.59308 86.06567 assigned negative charge : -535.9601 centred at (gu) : 92.38283 89.79436 85.86961 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 88945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32472 grid for indexing accessible points = 1.400000 m= 30983 mr = 61645 m= 4097 mr = 22243 m= 170 mr = 2251 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 518 time to turn everything in is 0.7400000 number of dielectric boundary points 38029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 275 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 27394 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) : 0.5735737 object centre at (A) : 6.874499 -1.369500 4.861501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4665255E-02 -3.4378655E-03 midg,1,midg; midg,igrid,midg 2.8720628E-02 1.3516752E-02 1,midg,midg; igrid,midg,midg -6.6955580E-04 3.5842333E-04 gauss-seidel spectral radius is 0.9984520 estimated iterations to convergence 202 setup time was (sec) 1.100000 now iterating at: 16:12:05 rms-change max change #iterations 4.170807 169.9628 at 10iterations 1.856333 72.16277 at 20iterations 0.8262025 30.27014 at 30iterations 0.3680550 11.37360 at 40iterations 0.1645774 4.905617 at 50iterations 7.3607408E-02 2.988787 at 60iterations 3.2827165E-02 1.090193 at 70iterations 1.4666931E-02 0.4731598 at 80iterations 6.5687899E-03 0.1984177 at 90iterations 2.9410392E-03 8.5938454E-02 at 100iterations 1.3265114E-03 4.2735100E-02 at 110iterations 6.0304441E-04 1.8463135E-02 at 120iterations finished qdiffx linear iterations at : 16:12:16 total time elapsed so far: 11.48000 # loops : 120 mean,max change (kT/e) : 6.0304441E-04 1.8463135E-02 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 16:12:16 11.652u 0.436s 0:12.55 96.2% 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 Mon Oct 10 2011 at 16:12:16 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 = 3636 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 has a net charge of 1.4000 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: 2.581082 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): -17.72100 31.47000 ymin,ymax (A): -32.40300 29.66400 zmin,zma (A): -25.90100 35.62400 x,y,z range (A): 49.19100 62.06700 61.52500 scale (grids/A): 2.581082 object centre (A): 6.874499 -1.369500 4.861501 number of atom coordinates read : 3636 total number of charged atoms : 3531 net assigned charge : 4.700007 assigned positive charge : 540.6578 centred at (gu) : 93.30598 89.38928 84.09827 assigned negative charge : -535.9601 centred at (gu) : 93.57412 89.69141 83.80434 start vw surface at 0.1400000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 206034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32472 grid for indexing accessible points = 1.400000 m= 102697 mr = 150086 m= 33921 mr = 82584 m= 6886 mr = 26496 m= 753 mr = 4851 m= 18 mr = 428 m= 0 mr = 0 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 1814 time to turn everything in is 1.850000 number of dielectric boundary points 85864 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 28234 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) : 1.720721 object centre at (A) : 6.874499 -1.369500 4.861501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4822651 -0.1196846 midg,1,midg; midg,igrid,midg 0.3368791 0.3538315 1,midg,midg; igrid,midg,midg -4.9569566E-02 1.2805668E-02 gauss-seidel spectral radius is 0.9992390 estimated iterations to convergence 286 setup time was (sec) 2.200000 now iterating at: 16:12:19 rms-change max change #iterations 10.36130 315.7067 at 10iterations 6.079591 135.2103 at 20iterations 3.542067 74.77581 at 30iterations 2.063676 39.89476 at 40iterations 1.190731 23.41883 at 50iterations 0.6879851 13.05049 at 60iterations 0.3962477 7.036445 at 70iterations 0.2284665 4.027859 at 80iterations 0.1309305 2.463150 at 90iterations 7.5279705E-02 1.322859 at 100iterations 4.3114442E-02 0.8036613 at 110iterations 2.4659602E-02 0.4085865 at 120iterations 1.4156293E-02 0.2573242 at 130iterations 8.0977604E-03 0.1398306 at 140iterations 4.6452326E-03 8.3303452E-02 at 150iterations 2.6593648E-03 4.8011780E-02 at 160iterations 1.5284476E-03 2.6948929E-02 at 170iterations 8.8167033E-04 1.5167236E-02 at 180iterations finished qdiffx linear iterations at : 16:12:36 total time elapsed so far: 19.53000 # loops : 180 mean,max change (kT/e) : 8.8167033E-04 1.5167236E-02 energy calculations done at 19.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.69000 DelPhi exited at 16:12:37 19.693u 0.480s 0:20.43 98.7% 0+0k 0+0io 0pf+0w