Tue Oct 11 03:14:01 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 Tue Oct 11 2011 at 03:14:01 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 = 2914 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6016156 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): -26.43300 25.13600 ymin,ymax (A): -38.09400 21.08000 zmin,zma (A): -23.80100 29.57500 x,y,z range (A): 51.56900 59.17400 53.37600 scale (grids/A): 0.6016156 object centre (A): -0.6485004 -8.506999 2.887000 number of atom coordinates read : 2914 total number of charged atoms : 2783 net assigned charge : 3.500021 assigned positive charge : 437.3452 centred at (gu) : 89.75409 93.14397 89.63700 assigned negative charge : -433.8464 centred at (gu) : 89.76983 93.20743 89.58474 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7176 nv = 96 ne = 84 npr = 57541 no. pairs analyzed = 57541 no. exposed pairs = 4114 no. arc points = 29123 no. surface atoms = 1347 nbur = 1567 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 337 mr = 3490 m= 0 mr = 13 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2200000 number of dielectric boundary points 4010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2915 ## 289 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8921 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1738620E-10 3.5608012E-09 midg,1,midg; midg,igrid,midg 2.1549955E-09 -2.3068911E-09 1,midg,midg; igrid,midg,midg 2.4614277E-09 9.4677233E-10 gauss-seidel spectral radius is 0.9857397 estimated iterations to convergence 69 setup time was (sec) 0.4100000 now iterating at: 03:14:01 rms-change max change #iterations 0.1152211 18.14019 at 10iterations 1.0232421E-02 1.559731 at 20iterations 1.4001933E-03 0.2181625 at 30iterations 4.0966738E-04 6.8006516E-02 at 40iterations 1.4574830E-04 2.4280548E-02 at 50iterations finished qdiffx linear iterations at : 03:14:04 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.4574830E-04 2.4280548E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 03:14:05 3.471u 0.171s 0:04.02 90.5% 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 Tue Oct 11 2011 at 03:14:05 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 = 2914 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.804847 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): -26.43300 25.13600 ymin,ymax (A): -38.09400 21.08000 zmin,zma (A): -23.80100 29.57500 x,y,z range (A): 51.56900 59.17400 53.37600 scale (grids/A): 1.804847 object centre (A): -0.6485004 -8.506999 2.887000 number of atom coordinates read : 2914 total number of charged atoms : 2783 net assigned charge : 3.500021 assigned positive charge : 437.3452 centred at (gu) : 89.26137 99.43111 88.91048 assigned negative charge : -433.8464 centred at (gu) : 89.30916 99.62219 88.75388 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29123 grid for indexing accessible points = 1.400000 m= 25464 mr = 50759 m= 3291 mr = 16959 m= 149 mr = 1584 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.3700000 number of dielectric boundary points 37227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 21708 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) : 0.6016156 object centre at (A) : -0.6485004 -8.506999 2.887000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5290570E-02 6.3437959E-03 midg,1,midg; midg,igrid,midg -4.5086863E-03 -1.2710609E-02 1,midg,midg; igrid,midg,midg 2.8603844E-02 -4.4837599E-03 gauss-seidel spectral radius is 0.9985397 estimated iterations to convergence 207 setup time was (sec) 0.6100000 now iterating at: 03:14:06 rms-change max change #iterations 4.080015 183.7933 at 10iterations 1.853501 68.58159 at 20iterations 0.8475932 30.31652 at 30iterations 0.3860721 12.49740 at 40iterations 0.1768111 6.104813 at 50iterations 8.0772571E-02 2.451902 at 60iterations 3.7103694E-02 1.208771 at 70iterations 1.6976038E-02 0.6225777 at 80iterations 7.8637674E-03 0.2584634 at 90iterations 3.7071854E-03 0.1264191 at 100iterations 1.8044134E-03 6.8737030E-02 at 110iterations 9.2504756E-04 3.2293320E-02 at 120iterations finished qdiffx linear iterations at : 03:14:13 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 9.2504756E-04 3.2293320E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 03:14:13 7.953u 0.211s 0:08.60 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 03:14:14 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 = 2914 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.707270 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): -26.43300 25.13600 ymin,ymax (A): -38.09400 21.08000 zmin,zma (A): -23.80100 29.57500 x,y,z range (A): 51.56900 59.17400 53.37600 scale (grids/A): 2.707270 object centre (A): -0.6485004 -8.506999 2.887000 number of atom coordinates read : 2914 total number of charged atoms : 2783 net assigned charge : 3.500021 assigned positive charge : 437.3452 centred at (gu) : 88.89195 104.1467 88.36552 assigned negative charge : -433.8464 centred at (gu) : 88.96381 104.4334 88.13075 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 179898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29123 grid for indexing accessible points = 1.400000 m= 83723 mr = 124655 m= 27563 mr = 64608 m= 5479 mr = 20359 m= 529 mr = 3488 m= 20 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 180 time to turn everything in is 0.9600000 number of dielectric boundary points 83880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 22263 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) : 1.804847 object centre at (A) : -0.6485004 -8.506999 2.887000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2555657 8.9307554E-02 midg,1,midg; midg,igrid,midg -0.1538905 -0.2751860 1,midg,midg; igrid,midg,midg 0.3647506 -8.0577239E-02 gauss-seidel spectral radius is 0.9992652 estimated iterations to convergence 291 setup time was (sec) 1.200000 now iterating at: 03:14:15 rms-change max change #iterations 10.11898 369.7112 at 10iterations 6.041613 158.7154 at 20iterations 3.580150 95.18463 at 30iterations 2.109795 58.16519 at 40iterations 1.236761 30.12885 at 50iterations 0.7225834 18.10244 at 60iterations 0.4206603 8.751232 at 70iterations 0.2441278 5.183899 at 80iterations 0.1419069 2.943823 at 90iterations 8.2129031E-02 1.803757 at 100iterations 4.7650401E-02 0.9820118 at 110iterations 2.7570907E-02 0.5385017 at 120iterations 1.5946696E-02 0.3412895 at 130iterations 9.2303073E-03 0.1849823 at 140iterations 5.3629284E-03 0.1033425 at 150iterations 3.1211516E-03 6.6394806E-02 at 160iterations 1.8324786E-03 3.8448334E-02 at 170iterations 1.0933171E-03 2.2539854E-02 at 180iterations finished qdiffx linear iterations at : 03:14:26 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 1.0933171E-03 2.2539854E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 03:14:27 12.827u 0.216s 0:13.38 97.3% 0+0k 0+0io 0pf+0w