Sun Oct 9 12:35:37 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+sph.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 = amb.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 12:35:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 0.7046295 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): -6.076000 43.88200 ymin,ymax (A): -14.37200 36.15100 zmin,zma (A): 0.8210000 45.40300 x,y,z range (A): 49.95800 50.52300 44.58200 scale (grids/A): 0.7046295 object centre (A): 18.90300 10.88950 23.11200 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 363.7711 centred at (gu) : 89.65012 91.30608 90.86975 assigned negative charge : -359.2716 centred at (gu) : 89.64946 91.47324 90.94167 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8038 nv = 96 ne = 84 npr = 47831 no. pairs analyzed = 47831 no. exposed pairs = 2993 no. arc points = 21142 no. surface atoms = 997 nbur = 1386 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 489 mr = 4477 m= 5 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 71 time to turn everything in is 0.1900000 number of dielectric boundary points 3979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1939 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8941 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3600957E-08 -2.1165214E-09 midg,1,midg; midg,igrid,midg 9.6729551E-08 -7.0296814E-08 1,midg,midg; igrid,midg,midg 3.9384030E-08 3.5164305E-08 gauss-seidel spectral radius is 0.9895345 estimated iterations to convergence 80 setup time was (sec) 0.3900000 now iterating at: 12:35:38 rms-change max change #iterations 0.2106505 34.78659 at 10iterations 2.6441196E-02 3.691666 at 20iterations 3.6715602E-03 0.4142838 at 30iterations 8.2479621E-04 0.1296024 at 40iterations 2.7686488E-04 4.6974182E-02 at 50iterations finished qdiffx linear iterations at : 12:35:41 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.7686488E-04 4.6974182E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 12:35:41 3.418u 0.170s 0:03.86 92.7% 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 Sun Oct 9 2011 at 12:35:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 2.113889 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): -6.076000 43.88200 ymin,ymax (A): -14.37200 36.15100 zmin,zma (A): 0.8210000 45.40300 x,y,z range (A): 49.95800 50.52300 44.58200 scale (grids/A): 2.113889 object centre (A): 18.90300 10.88950 23.11200 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 363.7711 centred at (gu) : 88.95010 93.91769 92.60886 assigned negative charge : -359.2716 centred at (gu) : 88.94823 94.41958 92.82469 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 84756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21142 grid for indexing accessible points = 1.400000 m= 33063 mr = 58913 m= 6098 mr = 24770 m= 570 mr = 4039 m= 5 mr = 294 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 874 time to turn everything in is 0.4100000 number of dielectric boundary points 36476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17795 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) : 0.7046295 object centre at (A) : 18.90300 10.88950 23.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0307849E-02 2.6045009E-02 midg,1,midg; midg,igrid,midg 1.7462788E-02 -5.9684355E-02 1,midg,midg; igrid,midg,midg 6.4011507E-02 -3.9310250E-03 gauss-seidel spectral radius is 0.9988590 estimated iterations to convergence 234 setup time was (sec) 0.6300000 now iterating at: 12:35:42 rms-change max change #iterations 4.994492 194.5213 at 10iterations 2.476931 83.45905 at 20iterations 1.234451 36.37325 at 30iterations 0.6169979 18.36352 at 40iterations 0.3082488 9.315969 at 50iterations 0.1538642 4.382820 at 60iterations 7.7392630E-02 2.163612 at 70iterations 3.8658977E-02 1.101810 at 80iterations 1.9503228E-02 0.5483582 at 90iterations 9.9180415E-03 0.2841187 at 100iterations 5.1069423E-03 0.1619034 at 110iterations 2.7079466E-03 8.1863403E-02 at 120iterations finished qdiffx linear iterations at : 12:35:49 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.7079466E-03 8.1863403E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 12:35:50 7.979u 0.221s 0:08.47 96.6% 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 Sun Oct 9 2011 at 12:35:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 3.170833 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): -6.076000 43.88200 ymin,ymax (A): -14.37200 36.15100 zmin,zma (A): 0.8210000 45.40300 x,y,z range (A): 49.95800 50.52300 44.58200 scale (grids/A): 3.170833 object centre (A): 18.90300 10.88950 23.11200 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 363.7711 centred at (gu) : 88.42498 95.87640 93.91314 assigned negative charge : -359.2716 centred at (gu) : 88.42245 96.62926 94.23709 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 195358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21142 grid for indexing accessible points = 1.400000 m= 103601 mr = 142203 m= 41112 mr = 85408 m= 11341 mr = 33637 m= 2318 mr = 8802 m= 312 mr = 1646 m= 6 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2893 time to turn everything in is 1.300000 number of dielectric boundary points 82149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 17932 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) : 2.113889 object centre at (A) : 18.90300 10.88950 23.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4969210 0.1209633 midg,1,midg; midg,igrid,midg 0.3118681 -0.6821668 1,midg,midg; igrid,midg,midg 0.7763444 -0.3324524 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 1.530000 now iterating at: 12:35:51 rms-change max change #iterations 11.07423 430.1255 at 10iterations 6.575521 135.4453 at 20iterations 3.890583 72.05170 at 30iterations 2.300967 41.59953 at 40iterations 1.359248 25.60706 at 50iterations 0.8007786 13.03105 at 60iterations 0.4704488 7.823494 at 70iterations 0.2768987 5.171042 at 80iterations 0.1628571 2.687471 at 90iterations 9.5770575E-02 1.602600 at 100iterations 5.6419861E-02 0.9302235 at 110iterations 3.3349022E-02 0.6020889 at 120iterations 1.9837495E-02 0.3619699 at 130iterations 1.1938130E-02 0.2526646 at 140iterations 7.4137845E-03 0.1374149 at 150iterations 4.7911778E-03 9.6223831E-02 at 160iterations 3.2860211E-03 6.5044403E-02 at 170iterations 2.4083811E-03 5.1210403E-02 at 180iterations finished qdiffx linear iterations at : 12:36:03 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 2.4083811E-03 5.1210403E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 12:36:03 13.180u 0.223s 0:13.66 98.0% 0+0k 0+0io 0pf+0w