Sat Oct 8 16:26:11 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 Sat Oct 8 2011 at 16:26:11 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 0.6615871 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): -1.935000 47.62700 ymin,ymax (A): -16.25900 29.16900 zmin,zma (A): -17.44200 36.36800 x,y,z range (A): 49.56200 45.42800 53.81000 scale (grids/A): 0.6615871 object centre (A): 22.84600 6.454999 9.463000 number of atom coordinates read : 2286 total number of charged atoms : 2223 net assigned charge : 3.806002 assigned positive charge : 342.9682 centred at (gu) : 89.99796 88.81744 89.83656 assigned negative charge : -339.1628 centred at (gu) : 90.04297 88.92029 89.88290 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6767 nv = 96 ne = 84 npr = 45708 no. pairs analyzed = 45708 no. exposed pairs = 2948 no. arc points = 20389 no. surface atoms = 1011 nbur = 1275 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 3726 m= 4 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3500000 number of dielectric boundary points 3409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1940 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8119 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8757069E-08 1.4289711E-09 midg,1,midg; midg,igrid,midg 3.6045694E-08 -6.8049455E-09 1,midg,midg; igrid,midg,midg 1.7907055E-08 1.7017905E-09 gauss-seidel spectral radius is 0.9881321 estimated iterations to convergence 75 setup time was (sec) 0.7000000 now iterating at: 16:26:12 rms-change max change #iterations 0.1551436 24.67706 at 10iterations 1.6897073E-02 2.384514 at 20iterations 1.7842087E-03 0.2544098 at 30iterations 2.0554313E-04 2.8434753E-02 at 40iterations 3.1131171E-05 5.1976442E-03 at 50iterations finished qdiffx linear iterations at : 16:26:16 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 3.1131171E-05 5.1976442E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 16:26:16 4.462u 0.420s 0:05.19 94.0% 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 Sat Oct 8 2011 at 16:26:16 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 1.984761 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): -1.935000 47.62700 ymin,ymax (A): -16.25900 29.16900 zmin,zma (A): -17.44200 36.36800 x,y,z range (A): 49.56200 45.42800 53.81000 scale (grids/A): 1.984761 object centre (A): 22.84600 6.454999 9.463000 number of atom coordinates read : 2286 total number of charged atoms : 2223 net assigned charge : 3.806002 assigned positive charge : 342.9682 centred at (gu) : 89.99327 86.45181 89.50919 assigned negative charge : -339.1628 centred at (gu) : 90.12890 86.76079 89.64863 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20389 grid for indexing accessible points = 1.400000 m= 27197 mr = 50253 m= 5202 mr = 20099 m= 387 mr = 3450 m= 5 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1215 time to turn everything in is 0.7500000 number of dielectric boundary points 31360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 17580 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) : 0.6615871 object centre at (A) : 22.84600 6.454999 9.463000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4584500E-02 -8.6779669E-03 midg,1,midg; midg,igrid,midg 2.2674708E-02 -4.5008594E-03 1,midg,midg; igrid,midg,midg 7.1296808E-03 -3.7060950E-02 gauss-seidel spectral radius is 0.9987096 estimated iterations to convergence 221 setup time was (sec) 1.080000 now iterating at: 16:26:18 rms-change max change #iterations 4.297611 153.5439 at 10iterations 2.048691 79.08146 at 20iterations 0.9787300 31.38691 at 30iterations 0.4691108 15.11346 at 40iterations 0.2244545 7.235871 at 50iterations 0.1078426 3.464005 at 60iterations 5.1576573E-02 1.658115 at 70iterations 2.4696451E-02 0.7976565 at 80iterations 1.1825738E-02 0.3621578 at 90iterations 5.6603351E-03 0.1799088 at 100iterations 2.7134405E-03 8.3215714E-02 at 110iterations 1.3039828E-03 4.2482376E-02 at 120iterations finished qdiffx linear iterations at : 16:26:27 total time elapsed so far: 10.22000 # loops : 120 mean,max change (kT/e) : 1.3039828E-03 4.2482376E-02 energy calculations done at 10.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.43000 DelPhi exited at 16:26:27 10.436u 0.498s 0:11.20 97.5% 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 Sat Oct 8 2011 at 16:26:27 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 2.977142 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): -1.935000 47.62700 ymin,ymax (A): -16.25900 29.16900 zmin,zma (A): -17.44200 36.36800 x,y,z range (A): 49.56200 45.42800 53.81000 scale (grids/A): 2.977142 object centre (A): 22.84600 6.454999 9.463000 number of atom coordinates read : 2286 total number of charged atoms : 2223 net assigned charge : 3.806002 assigned positive charge : 342.9682 centred at (gu) : 89.98981 84.67754 89.26370 assigned negative charge : -339.1628 centred at (gu) : 90.19316 85.14117 89.47285 start vw surface at 0.1500000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 167939 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20389 grid for indexing accessible points = 1.400000 m= 85442 mr = 122050 m= 33776 mr = 69674 m= 9790 mr = 27490 m= 1728 mr = 7592 m= 143 mr = 1205 m= 5 mr = 85 m= 0 mr = 2 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 3955 time to turn everything in is 2.040000 number of dielectric boundary points 70725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 17784 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) : 1.984761 object centre at (A) : 22.84600 6.454999 9.463000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3707028 -0.1817673 midg,1,midg; midg,igrid,midg 0.1694262 -7.1393244E-02 1,midg,midg; igrid,midg,midg 5.2086670E-02 -0.5060475 gauss-seidel spectral radius is 0.9992789 estimated iterations to convergence 294 setup time was (sec) 2.400000 now iterating at: 16:26:30 rms-change max change #iterations 9.939322 370.4147 at 10iterations 5.864308 162.9595 at 20iterations 3.455608 74.06194 at 30iterations 2.029620 40.71390 at 40iterations 1.185989 22.20932 at 50iterations 0.6925628 13.30982 at 60iterations 0.4035540 7.549678 at 70iterations 0.2354785 4.099074 at 80iterations 0.1369950 2.486515 at 90iterations 7.9370260E-02 1.441949 at 100iterations 4.6039026E-02 0.8016014 at 110iterations 2.6780233E-02 0.4631090 at 120iterations 1.5553870E-02 0.2858553 at 130iterations 9.0064164E-03 0.1560745 at 140iterations 5.2325898E-03 9.8906517E-02 at 150iterations 3.0416781E-03 5.5118084E-02 at 160iterations 1.7735801E-03 3.2363892E-02 at 170iterations 1.0389551E-03 2.1785736E-02 at 180iterations finished qdiffx linear iterations at : 16:26:46 total time elapsed so far: 17.69000 # loops : 180 mean,max change (kT/e) : 1.0389551E-03 2.1785736E-02 energy calculations done at 17.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.92000 DelPhi exited at 16:26:46 17.924u 0.494s 0:18.69 98.5% 0+0k 0+0io 0pf+0w