Tue Nov 22 14:13:23 PST 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 Nov 22 2011 at 14:13:32 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 0.6325403 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 0.6325403 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 288.8440 centred at (gu) : 90.63264 89.97509 90.50941 assigned negative charge : -285.8443 centred at (gu) : 90.54665 90.12145 90.50598 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5260 nv = 96 ne = 84 npr = 39877 no. pairs analyzed = 39877 no. exposed pairs = 2447 no. arc points = 17104 no. surface atoms = 831 nbur = 1111 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 309 mr = 2895 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1696 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9155138E-09 4.1394927E-09 midg,1,midg; midg,igrid,midg 1.3628398E-08 -6.8868484E-09 1,midg,midg; igrid,midg,midg -2.2327591E-09 1.0826635E-08 gauss-seidel spectral radius is 0.9869956 estimated iterations to convergence 72 setup time was (sec) 0.4400000 now iterating at: 14:13:37 rms-change max change #iterations 0.1187463 20.56074 at 10iterations 1.1383616E-02 1.879902 at 20iterations 1.0756839E-03 0.1945496 at 30iterations 1.0210640E-04 1.7609119E-02 at 40iterations 9.7518623E-06 1.5835762E-03 at 50iterations finished qdiffx linear iterations at : 14:13:44 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 9.7518623E-06 1.5835762E-03 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 14:13:46 3.032u 0.137s 0:15.20 20.7% 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 Nov 22 2011 at 14:13:49 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.897621 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 1.897621 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 288.8440 centred at (gu) : 91.89806 89.92541 91.52814 assigned negative charge : -285.8443 centred at (gu) : 91.64017 90.36448 91.51801 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 56508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17104 grid for indexing accessible points = 1.400000 m= 21108 mr = 38804 m= 3386 mr = 15964 m= 187 mr = 2160 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 24205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14214 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) : 0.6325403 object centre at (A) : -12.66050 20.18500 27.22350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3980824E-02 3.4332238E-02 midg,1,midg; midg,igrid,midg 3.1856610E-03 -9.9714790E-03 1,midg,midg; igrid,midg,midg -3.9901454E-03 -1.4411911E-03 gauss-seidel spectral radius is 0.9985476 estimated iterations to convergence 208 setup time was (sec) 0.6800000 now iterating at: 14:13:54 rms-change max change #iterations 3.574526 167.1700 at 10iterations 1.638587 65.73902 at 20iterations 0.7489080 27.31993 at 30iterations 0.3429680 11.45646 at 40iterations 0.1564133 5.496312 at 50iterations 7.1630970E-02 2.696188 at 60iterations 3.2607827E-02 1.144718 at 70iterations 1.4952449E-02 0.5536475 at 80iterations 6.8068500E-03 0.2489319 at 90iterations 3.1223965E-03 0.1106644 at 100iterations 1.4239297E-03 5.3153753E-02 at 110iterations 6.5314682E-04 2.3167133E-02 at 120iterations finished qdiffx linear iterations at : 14:14:14 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 6.5314682E-04 2.3167133E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 14:14:23 7.430u 0.275s 0:34.72 22.1% 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 Nov 22 2011 at 14:14:26 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 2.846431 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 2.846431 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 288.8440 centred at (gu) : 92.84700 89.88808 92.29225 assigned negative charge : -285.8443 centred at (gu) : 92.46031 90.54678 92.27710 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 130720 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17104 grid for indexing accessible points = 1.400000 m= 67757 mr = 94022 m= 25299 mr = 56053 m= 6103 mr = 20816 m= 865 mr = 4633 m= 57 mr = 603 m= 4 mr = 28 m= 0 mr = 2 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 54648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 14471 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) : 1.897621 object centre at (A) : -12.66050 20.18500 27.22350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6191385E-02 0.1962524 midg,1,midg; midg,igrid,midg -3.2744016E-02 -0.1358812 1,midg,midg; igrid,midg,midg -7.0596375E-02 -6.9080919E-02 gauss-seidel spectral radius is 0.9992184 estimated iterations to convergence 282 setup time was (sec) 1.290000 now iterating at: 14:14:32 rms-change max change #iterations 8.372837 393.1074 at 10iterations 4.769198 101.0726 at 20iterations 2.702264 64.30573 at 30iterations 1.530754 44.01035 at 40iterations 0.8644523 20.94053 at 50iterations 0.4883843 10.08900 at 60iterations 0.2759116 5.492615 at 70iterations 0.1555868 3.480972 at 80iterations 8.8038363E-02 1.773052 at 90iterations 4.9695980E-02 1.031094 at 100iterations 2.8154286E-02 0.5639305 at 110iterations 1.5852612E-02 0.3329172 at 120iterations 8.9720497E-03 0.1925859 at 130iterations 5.0525083E-03 0.1053505 at 140iterations 2.8577566E-03 5.7582855E-02 at 150iterations 1.6092198E-03 3.3381462E-02 at 160iterations 9.0915099E-04 1.9577026E-02 at 170iterations 5.1303772E-04 1.1631012E-02 at 180iterations finished qdiffx linear iterations at : 14:15:00 total time elapsed so far: 10.60000 # loops : 180 mean,max change (kT/e) : 5.1303772E-04 1.1631012E-02 energy calculations done at 10.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.78000 DelPhi exited at 14:15:03 10.778u 0.171s 0:37.71 29.0% 0+0k 0+0io 0pf+0w