Tue Oct 11 03:48:37 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 03:48:37 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 0.6622517 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): -9.570000 36.58400 ymin,ymax (A): -26.41400 21.77800 zmin,zma (A): -8.117000 45.63900 x,y,z range (A): 46.15400 48.19200 53.75600 scale (grids/A): 0.6622517 object centre (A): 13.50700 -2.318000 18.76100 number of atom coordinates read : 2754 total number of charged atoms : 2596 net assigned charge : 2.926017 assigned positive charge : 420.3398 centred at (gu) : 89.42489 90.32286 91.32362 assigned negative charge : -417.4142 centred at (gu) : 89.16113 90.16344 91.31163 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8133 nv = 96 ne = 84 npr = 55842 no. pairs analyzed = 55842 no. exposed pairs = 3301 no. arc points = 22888 no. surface atoms = 1102 nbur = 1652 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4725 m= 4 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2100000 number of dielectric boundary points 3801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2217 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9516 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2744146E-09 1.4311172E-08 midg,1,midg; midg,igrid,midg -2.6351907E-08 4.6524164E-08 1,midg,midg; igrid,midg,midg -5.9727995E-08 5.8439806E-08 gauss-seidel spectral radius is 0.9881921 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 03:48:37 rms-change max change #iterations 0.1797018 25.91313 at 10iterations 1.9821187E-02 2.706565 at 20iterations 2.1368361E-03 0.2834816 at 30iterations 2.6194178E-04 3.4582138E-02 at 40iterations 4.4134602E-05 7.3604584E-03 at 50iterations finished qdiffx linear iterations at : 03:48:40 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 4.4134602E-05 7.3604584E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 03:48:41 3.353u 0.161s 0:03.93 89.3% 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 03:48:41 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 1.986755 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): -9.570000 36.58400 ymin,ymax (A): -26.41400 21.77800 zmin,zma (A): -8.117000 45.63900 x,y,z range (A): 46.15400 48.19200 53.75600 scale (grids/A): 1.986755 object centre (A): 13.50700 -2.318000 18.76100 number of atom coordinates read : 2754 total number of charged atoms : 2596 net assigned charge : 2.926017 assigned positive charge : 420.3398 centred at (gu) : 88.27436 90.96810 93.97059 assigned negative charge : -417.4142 centred at (gu) : 87.48285 90.48978 93.93468 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 87048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22888 grid for indexing accessible points = 1.400000 m= 33799 mr = 62212 m= 5948 mr = 25804 m= 431 mr = 4050 m= 6 mr = 224 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 371 time to turn everything in is 0.4200000 number of dielectric boundary points 34942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20505 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) : 0.6622517 object centre at (A) : 13.50700 -2.318000 18.76100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8996513E-03 1.0896876E-02 midg,1,midg; midg,igrid,midg -2.3063693E-02 9.0155909E-03 1,midg,midg; igrid,midg,midg -2.8643126E-02 6.3933842E-02 gauss-seidel spectral radius is 0.9987538 estimated iterations to convergence 224 setup time was (sec) 0.6300000 now iterating at: 03:48:42 rms-change max change #iterations 4.851427 231.5635 at 10iterations 2.348613 73.08295 at 20iterations 1.143945 33.56786 at 30iterations 0.5527861 15.51611 at 40iterations 0.2694788 7.456259 at 50iterations 0.1305213 4.009900 at 60iterations 6.3484102E-02 1.990785 at 70iterations 3.0740324E-02 0.8812115 at 80iterations 1.4969645E-02 0.4155502 at 90iterations 7.2650411E-03 0.2033775 at 100iterations 3.5302017E-03 0.1011086 at 110iterations 1.7208724E-03 4.8006058E-02 at 120iterations finished qdiffx linear iterations at : 03:48:49 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.7208724E-03 4.8006058E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 03:48:49 7.760u 0.197s 0:08.49 93.6% 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 03:48:49 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 2.980132 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): -9.570000 36.58400 ymin,ymax (A): -26.41400 21.77800 zmin,zma (A): -8.117000 45.63900 x,y,z range (A): 46.15400 48.19200 53.75600 scale (grids/A): 2.980132 object centre (A): 13.50700 -2.318000 18.76100 number of atom coordinates read : 2754 total number of charged atoms : 2596 net assigned charge : 2.926017 assigned positive charge : 420.3398 centred at (gu) : 87.41145 91.45214 95.95558 assigned negative charge : -417.4142 centred at (gu) : 86.22417 90.73459 95.90177 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 201111 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22888 grid for indexing accessible points = 1.400000 m= 107256 mr = 149748 m= 41596 mr = 89676 m= 11101 mr = 34428 m= 1885 mr = 8792 m= 165 mr = 1443 m= 1 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 1363 time to turn everything in is 1.110000 number of dielectric boundary points 78924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 20760 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) : 1.986755 object centre at (A) : 13.50700 -2.318000 18.76100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6101993E-02 0.2976761 midg,1,midg; midg,igrid,midg -0.2416307 6.3150883E-02 1,midg,midg; igrid,midg,midg -0.2265480 0.5585526 gauss-seidel spectral radius is 0.9992852 estimated iterations to convergence 295 setup time was (sec) 1.320000 now iterating at: 03:48:51 rms-change max change #iterations 11.08533 376.5961 at 10iterations 6.508348 146.7882 at 20iterations 3.812901 75.73207 at 30iterations 2.228699 45.10833 at 40iterations 1.304377 24.54441 at 50iterations 0.7615382 13.69649 at 60iterations 0.4437055 7.499422 at 70iterations 0.2589428 4.609238 at 80iterations 0.1506592 2.808832 at 90iterations 8.7701350E-02 1.453300 at 100iterations 5.0946709E-02 0.8521395 at 110iterations 2.9603478E-02 0.4770126 at 120iterations 1.7209861E-02 0.2835064 at 130iterations 1.0029620E-02 0.1688783 at 140iterations 5.8285510E-03 9.6372604E-02 at 150iterations 3.3974813E-03 6.2942505E-02 at 160iterations 1.9888575E-03 3.3723831E-02 at 170iterations 1.1763022E-03 2.0858765E-02 at 180iterations finished qdiffx linear iterations at : 03:49:02 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 1.1763022E-03 2.0858765E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 03:49:03 12.740u 0.218s 0:13.25 97.7% 0+0k 0+0io 0pf+0w