Tue Oct 11 03:35:20 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 03:35:20 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2216 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 has a net charge of 0.5140 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: 0.6066079 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): 20.75100 70.84900 ymin,ymax (A): -15.72000 33.65300 zmin,zma (A): -9.669001 49.01800 x,y,z range (A): 50.09800 49.37300 58.68700 scale (grids/A): 0.6066079 object centre (A): 45.80000 8.966500 19.67450 number of atom coordinates read : 2216 total number of charged atoms : 2116 net assigned charge : -4.585982 assigned positive charge : 329.7004 centred at (gu) : 90.64799 89.43242 90.60977 assigned negative charge : -334.2867 centred at (gu) : 90.57542 89.58489 90.63381 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5437 nv = 96 ne = 84 npr = 45409 no. pairs analyzed = 45409 no. exposed pairs = 2837 no. arc points = 20396 no. surface atoms = 957 nbur = 1259 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 263 mr = 2794 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2900000 number of dielectric boundary points 2889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1982 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6726 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3654725E-09 -3.8936454E-09 midg,1,midg; midg,igrid,midg 3.7673162E-09 -7.4318383E-09 1,midg,midg; igrid,midg,midg -4.5786139E-09 3.6356645E-10 gauss-seidel spectral radius is 0.9859046 estimated iterations to convergence 69 setup time was (sec) 0.5000000 now iterating at: 03:35:21 rms-change max change #iterations 0.1030759 16.04660 at 10iterations 9.0653133E-03 1.395927 at 20iterations 8.0124068E-04 0.1272602 at 30iterations 6.8965986E-05 1.1222839E-02 at 40iterations 5.9317390E-06 9.8419189E-04 at 50iterations finished qdiffx linear iterations at : 03:35:24 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 5.9317390E-06 9.8419189E-04 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 03:35:24 3.175u 0.145s 0:03.85 85.9% 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 Tue Oct 11 2011 at 03:35:24 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2216 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 has a net charge of 0.5140 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: 1.819824 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): 20.75100 70.84900 ymin,ymax (A): -15.72000 33.65300 zmin,zma (A): -9.669001 49.01800 x,y,z range (A): 50.09800 49.37300 58.68700 scale (grids/A): 1.819824 object centre (A): 45.80000 8.966500 19.67450 number of atom coordinates read : 2216 total number of charged atoms : 2116 net assigned charge : -4.585982 assigned positive charge : 329.7004 centred at (gu) : 91.94370 88.29712 91.82907 assigned negative charge : -334.2867 centred at (gu) : 91.72611 88.75448 91.90129 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 58752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20396 grid for indexing accessible points = 1.400000 m= 19704 mr = 39183 m= 2918 mr = 13922 m= 131 mr = 1668 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 50 time to turn everything in is 0.4300000 number of dielectric boundary points 26699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 16552 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) : 0.6066079 object centre at (A) : 45.80000 8.966500 19.67450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2460144E-02 1.7558469E-03 midg,1,midg; midg,igrid,midg 1.7865548E-02 -2.2633428E-02 1,midg,midg; igrid,midg,midg -1.2412486E-02 1.4807793E-03 gauss-seidel spectral radius is 0.9984732 estimated iterations to convergence 203 setup time was (sec) 0.7000000 now iterating at: 03:35:25 rms-change max change #iterations 3.527232 167.0556 at 10iterations 1.576486 59.15571 at 20iterations 0.7076716 27.92319 at 30iterations 0.3159880 12.05007 at 40iterations 0.1416762 5.711723 at 50iterations 6.3131936E-02 2.325397 at 60iterations 2.8315641E-02 1.063108 at 70iterations 1.2660649E-02 0.4624214 at 80iterations 5.6754816E-03 0.2168884 at 90iterations 2.5389264E-03 9.1404915E-02 at 100iterations 1.1402138E-03 4.2250156E-02 at 110iterations 5.0908152E-04 1.8878937E-02 at 120iterations finished qdiffx linear iterations at : 03:35:31 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 5.0908152E-04 1.8878937E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 03:35:32 6.918u 0.167s 0:07.45 94.8% 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 03:35:32 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2216 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 has a net charge of 0.5140 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: 2.729736 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): 20.75100 70.84900 ymin,ymax (A): -15.72000 33.65300 zmin,zma (A): -9.669001 49.01800 x,y,z range (A): 50.09800 49.37300 58.68700 scale (grids/A): 2.729736 object centre (A): 45.80000 8.966500 19.67450 number of atom coordinates read : 2216 total number of charged atoms : 2116 net assigned charge : -4.585982 assigned positive charge : 329.7004 centred at (gu) : 92.91549 87.44550 92.74348 assigned negative charge : -334.2867 centred at (gu) : 92.58921 88.13167 92.85184 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 135920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20396 grid for indexing accessible points = 1.400000 m= 64246 mr = 95402 m= 22634 mr = 51244 m= 5017 mr = 17567 m= 523 mr = 3614 m= 21 mr = 316 m= 0 mr = 4 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 1.040000 number of dielectric boundary points 60214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 16925 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) : 1.819824 object centre at (A) : 45.80000 8.966500 19.67450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3591478 9.3017034E-02 midg,1,midg; midg,igrid,midg 0.3289445 -0.2379717 1,midg,midg; igrid,midg,midg -7.2122797E-02 6.4366490E-02 gauss-seidel spectral radius is 0.9992099 estimated iterations to convergence 281 setup time was (sec) 1.340000 now iterating at: 03:35:33 rms-change max change #iterations 8.432997 282.0405 at 10iterations 4.782461 111.0422 at 20iterations 2.694475 58.30272 at 30iterations 1.516840 34.28335 at 40iterations 0.8547028 18.66658 at 50iterations 0.4816571 9.927341 at 60iterations 0.2698586 5.906921 at 70iterations 0.1519772 3.331017 at 80iterations 8.5219122E-02 1.654655 at 90iterations 4.7907107E-02 0.9704852 at 100iterations 2.6946656E-02 0.5777473 at 110iterations 1.5172758E-02 0.3014128 at 120iterations 8.5348496E-03 0.1824613 at 130iterations 4.8014377E-03 9.5535278E-02 at 140iterations 2.6945507E-03 5.7888031E-02 at 150iterations 1.5189954E-03 3.1985283E-02 at 160iterations 8.5435511E-04 1.7747879E-02 at 170iterations 4.7916494E-04 9.6111298E-03 at 180iterations finished qdiffx linear iterations at : 03:35:43 total time elapsed so far: 10.94000 # loops : 180 mean,max change (kT/e) : 4.7916494E-04 9.6111298E-03 energy calculations done at 10.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 03:35:44 11.126u 0.233s 0:11.81 96.1% 0+0k 0+0io 0pf+0w