Sun Oct 9 18:24:15 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 Sun Oct 9 2011 at 18:24:15 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5111 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5477934 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): 3.271000 68.25900 ymin,ymax (A): -9.157000 52.25200 zmin,zma (A): -1.995000 61.80700 x,y,z range (A): 64.98801 61.40900 63.80200 scale (grids/A): 0.5477934 object centre (A): 35.76500 21.54750 29.90600 number of atom coordinates read : 5111 total number of charged atoms : 4966 net assigned charge : 2.635050 assigned positive charge : 787.0206 centred at (gu) : 87.83276 89.64460 89.49678 assigned negative charge : -784.3918 centred at (gu) : 87.73122 89.69122 89.47937 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10072 nv = 96 ne = 84 npr = 103067 no. pairs analyzed = 103067 no. exposed pairs = 5974 no. arc points = 40724 no. surface atoms = 2049 nbur = 3062 mkacc time = 0.2400000 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 = 1.568000 m= 457 mr = 5746 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4102 ## 436 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 13159 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4980878E-11 3.7277154E-10 midg,1,midg; midg,igrid,midg 8.5517776E-10 -3.4608860E-10 1,midg,midg; igrid,midg,midg -1.8769599E-09 8.5302071E-10 gauss-seidel spectral radius is 0.9829734 estimated iterations to convergence 63 setup time was (sec) 0.7200000 now iterating at: 18:24:16 rms-change max change #iterations 0.1031000 13.13913 at 10iterations 9.5073031E-03 1.347759 at 20iterations 2.8106989E-03 0.3089447 at 30iterations 1.2746613E-03 0.1464872 at 40iterations 6.0020754E-04 7.3951721E-02 at 50iterations finished qdiffx linear iterations at : 18:24:19 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 6.0020754E-04 7.3951721E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 18:24:19 3.536u 0.166s 0:03.97 92.9% 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 Sun Oct 9 2011 at 18:24:19 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5111 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.643380 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): 3.271000 68.25900 ymin,ymax (A): -9.157000 52.25200 zmin,zma (A): -1.995000 61.80700 x,y,z range (A): 64.98801 61.40900 63.80200 scale (grids/A): 1.643380 object centre (A): 35.76500 21.54750 29.90600 number of atom coordinates read : 5111 total number of charged atoms : 4966 net assigned charge : 2.635050 assigned positive charge : 787.0206 centred at (gu) : 83.49732 88.93224 88.48921 assigned negative charge : -784.3918 centred at (gu) : 83.19386 89.07366 88.43802 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 112381 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40724 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 39028 mr = 81510 m= 4589 mr = 28219 m= 140 mr = 2421 m= 0 mr = 14 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 43974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 413 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 38089 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) : 0.5477934 object centre at (A) : 35.76500 21.54750 29.90600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8108279E-02 -1.7765533E-02 midg,1,midg; midg,igrid,midg 1.7815728E-02 5.8381814E-03 1,midg,midg; igrid,midg,midg 1.0801796E-02 2.5246141E-02 gauss-seidel spectral radius is 0.9984064 estimated iterations to convergence 199 setup time was (sec) 1.100000 now iterating at: 18:24:21 rms-change max change #iterations 4.759388 180.8771 at 10iterations 2.103032 61.15638 at 20iterations 0.9282330 26.90987 at 30iterations 0.4088875 11.02920 at 40iterations 0.1814598 5.754971 at 50iterations 8.0399223E-02 2.401649 at 60iterations 3.6013804E-02 1.064625 at 70iterations 1.6423948E-02 0.4767265 at 80iterations 7.8736413E-03 0.2338715 at 90iterations 4.1614794E-03 0.1126938 at 100iterations 2.5321674E-03 6.8069458E-02 at 110iterations 1.7319602E-03 4.5786858E-02 at 120iterations finished qdiffx linear iterations at : 18:24:27 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.7319602E-03 4.5786858E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 18:24:28 7.789u 0.164s 0:08.24 96.3% 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 Sun Oct 9 2011 at 18:24:28 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5111 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.465070 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): 3.271000 68.25900 ymin,ymax (A): -9.157000 52.25200 zmin,zma (A): -1.995000 61.80700 x,y,z range (A): 64.98801 61.40900 63.80200 scale (grids/A): 2.465070 object centre (A): 35.76500 21.54750 29.90600 number of atom coordinates read : 5111 total number of charged atoms : 4966 net assigned charge : 2.635050 assigned positive charge : 787.0206 centred at (gu) : 80.24556 88.39812 87.73325 assigned negative charge : -784.3918 centred at (gu) : 79.79065 88.61063 87.65708 start vw surface at 0.2300000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 260965 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40724 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 131528 mr = 197994 m= 41458 mr = 107404 m= 7558 mr = 32193 m= 558 mr = 5102 m= 12 mr = 268 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.020000 number of dielectric boundary points 99118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 39674 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) : 1.643380 object centre at (A) : 35.76500 21.54750 29.90600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3154257 -0.3835268 midg,1,midg; midg,igrid,midg 0.1380842 -8.1493787E-02 1,midg,midg; igrid,midg,midg -1.8447703E-02 0.4132727 gauss-seidel spectral radius is 0.9992458 estimated iterations to convergence 287 setup time was (sec) 2.330000 now iterating at: 18:24:30 rms-change max change #iterations 12.09263 356.8188 at 10iterations 7.113703 142.2088 at 20iterations 4.167710 88.17062 at 30iterations 2.421120 45.06227 at 40iterations 1.405146 24.17471 at 50iterations 0.8111293 15.14212 at 60iterations 0.4687193 7.847065 at 70iterations 0.2697677 4.876514 at 80iterations 0.1553818 2.471046 at 90iterations 8.9338221E-02 1.512685 at 100iterations 5.1390581E-02 0.8590698 at 110iterations 2.9700406E-02 0.5468903 at 120iterations 1.7258503E-02 0.3095379 at 130iterations 1.0148645E-02 0.1902466 at 140iterations 6.1120950E-03 0.1127491 at 150iterations 3.8469834E-03 7.7080965E-02 at 160iterations 2.5812159E-03 5.0461769E-02 at 170iterations 1.8634730E-03 3.4280777E-02 at 180iterations finished qdiffx linear iterations at : 18:24:41 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.8634730E-03 3.4280777E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 18:24:41 13.088u 0.161s 0:13.51 98.0% 0+0k 0+0io 0pf+0w