Tue Oct 11 06:18:58 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 Tue Oct 11 2011 at 06:18:58 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2072 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7024606 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): -20.77800 29.90100 ymin,ymax (A): -11.89700 30.61000 zmin,zma (A): -8.871000 38.28400 x,y,z range (A): 50.67900 42.50700 47.15500 scale (grids/A): 0.7024606 object centre (A): 4.561501 9.356501 14.70650 number of atom coordinates read : 2072 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 316.9580 centred at (gu) : 91.12112 89.83720 91.03973 assigned negative charge : -311.0131 centred at (gu) : 91.04481 89.77467 90.93105 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7008 nv = 96 ne = 84 npr = 41303 no. pairs analyzed = 41303 no. exposed pairs = 2585 no. arc points = 17429 no. surface atoms = 883 nbur = 1189 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4021 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1674 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7759 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4215106E-09 1.1146444E-07 midg,1,midg; midg,igrid,midg 1.6327474E-08 6.8725662E-08 1,midg,midg; igrid,midg,midg 8.2612956E-09 9.5743232E-08 gauss-seidel spectral radius is 0.9894372 estimated iterations to convergence 79 setup time was (sec) 0.5800000 now iterating at: 06:18:59 rms-change max change #iterations 0.1969669 26.17844 at 10iterations 2.3809560E-02 3.399335 at 20iterations 3.3280740E-03 0.4139328 at 30iterations 6.1202428E-04 9.2987061E-02 at 40iterations 1.6730877E-04 1.9821167E-02 at 50iterations finished qdiffx linear iterations at : 06:19:02 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.6730877E-04 1.9821167E-02 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 06:19:03 4.091u 0.266s 0:04.78 91.0% 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 06:19:03 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2072 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.107382 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): -20.77800 29.90100 ymin,ymax (A): -11.89700 30.61000 zmin,zma (A): -8.871000 38.28400 x,y,z range (A): 50.67900 42.50700 47.15500 scale (grids/A): 2.107382 object centre (A): 4.561501 9.356501 14.70650 number of atom coordinates read : 2072 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 316.9580 centred at (gu) : 93.36333 89.51160 93.11953 assigned negative charge : -311.0131 centred at (gu) : 93.13454 89.32409 92.79321 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 74218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17429 grid for indexing accessible points = 1.400000 m= 30253 mr = 52884 m= 5623 mr = 22952 m= 443 mr = 3641 m= 11 mr = 194 m= 0 mr = 3 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 30874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15364 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) : 0.7024606 object centre at (A) : 4.561501 9.356501 14.70650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7067126E-02 2.8952369E-02 midg,1,midg; midg,igrid,midg 1.7340105E-02 2.3611521E-02 1,midg,midg; igrid,midg,midg 4.3248061E-02 3.7613738E-02 gauss-seidel spectral radius is 0.9988166 estimated iterations to convergence 230 setup time was (sec) 0.9900000 now iterating at: 06:19:04 rms-change max change #iterations 4.575125 216.8315 at 10iterations 2.251937 77.85995 at 20iterations 1.112872 36.69667 at 30iterations 0.5488102 17.70553 at 40iterations 0.2718920 8.952699 at 50iterations 0.1343273 3.968285 at 60iterations 6.6450231E-02 1.836496 at 70iterations 3.2993995E-02 1.038681 at 80iterations 1.6501579E-02 0.4922199 at 90iterations 8.3164517E-03 0.2415781 at 100iterations 4.2312290E-03 0.1304169 at 110iterations 2.2348848E-03 6.5635681E-02 at 120iterations finished qdiffx linear iterations at : 06:19:12 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 2.2348848E-03 6.5635681E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 06:19:13 9.658u 0.308s 0:10.46 95.1% 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 06:19:13 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2072 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.161072 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): -20.77800 29.90100 ymin,ymax (A): -11.89700 30.61000 zmin,zma (A): -8.871000 38.28400 x,y,z range (A): 50.67900 42.50700 47.15500 scale (grids/A): 3.161072 object centre (A): 4.561501 9.356501 14.70650 number of atom coordinates read : 2072 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 316.9580 centred at (gu) : 95.04527 89.26740 94.67926 assigned negative charge : -311.0131 centred at (gu) : 94.70179 88.98619 94.18987 start vw surface at 0.1300000 fill in re-entrant regions at 0.9500000 boundary points on vw surface= 171000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17429 grid for indexing accessible points = 1.400000 m= 93953 mr = 127072 m= 38108 mr = 78300 m= 10529 mr = 31283 m= 1884 mr = 8004 m= 190 mr = 1264 m= 11 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.210000 number of dielectric boundary points 69637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 15504 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) : 2.107382 object centre at (A) : 4.561501 9.356501 14.70650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4286313 0.2694801 midg,1,midg; midg,igrid,midg 0.1459970 0.1502782 1,midg,midg; igrid,midg,midg 0.3537978 0.1684158 gauss-seidel spectral radius is 0.9992951 estimated iterations to convergence 297 setup time was (sec) 2.530000 now iterating at: 06:19:16 rms-change max change #iterations 10.30005 456.5861 at 10iterations 6.098480 139.0926 at 20iterations 3.607622 69.87039 at 30iterations 2.129155 44.15603 at 40iterations 1.253134 25.70804 at 50iterations 0.7393979 13.58811 at 60iterations 0.4336379 8.495171 at 70iterations 0.2548935 5.142376 at 80iterations 0.1490559 2.796856 at 90iterations 8.7704770E-02 1.595940 at 100iterations 5.1438134E-02 0.9628427 at 110iterations 3.0428205E-02 0.5563469 at 120iterations 1.8143969E-02 0.3495789 at 130iterations 1.1039793E-02 0.1964359 at 140iterations 6.9125728E-03 0.1250610 at 150iterations 4.5137680E-03 8.1001282E-02 at 160iterations 3.1358995E-03 6.2751770E-02 at 170iterations 2.3038189E-03 4.1400909E-02 at 180iterations finished qdiffx linear iterations at : 06:19:30 total time elapsed so far: 16.70000 # loops : 180 mean,max change (kT/e) : 2.3038189E-03 4.1400909E-02 energy calculations done at 16.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.88000 DelPhi exited at 06:19:31 16.881u 0.367s 0:17.65 97.6% 0+0k 0+0io 0pf+0w