Tue Oct 11 01:39:30 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 01:39:30 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2642 !!! WARNING: GLM 266 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5919324 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): 18.09900 78.24100 ymin,ymax (A): -11.52600 44.24500 zmin,zma (A): -7.594000 35.28800 x,y,z range (A): 60.14201 55.77100 42.88200 scale (grids/A): 0.5919324 object centre (A): 48.17000 16.35950 13.84700 number of atom coordinates read : 2642 total number of charged atoms : 2495 net assigned charge : 4.906021 assigned positive charge : 398.4307 centred at (gu) : 88.22939 89.83791 89.69724 assigned negative charge : -393.5255 centred at (gu) : 88.52175 89.98785 89.86562 start vw surface at 0.2100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6022 nv = 96 ne = 84 npr = 53878 no. pairs analyzed = 53878 no. exposed pairs = 3139 no. arc points = 22230 no. surface atoms = 1060 nbur = 1582 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 259 mr = 3311 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3600000 number of dielectric boundary points 2939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2206 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6154531E-09 -3.2425467E-09 midg,1,midg; midg,igrid,midg 5.8748042E-09 -2.8255560E-09 1,midg,midg; igrid,midg,midg 1.4439901E-08 -4.7762794E-09 gauss-seidel spectral radius is 0.9852321 estimated iterations to convergence 68 setup time was (sec) 0.5900000 now iterating at: 01:39:30 rms-change max change #iterations 0.1057898 18.76563 at 10iterations 9.1222376E-03 1.533585 at 20iterations 1.0904752E-03 0.2274895 at 30iterations 2.1467211E-04 5.3092957E-02 at 40iterations 4.9804526E-05 1.2779236E-02 at 50iterations finished qdiffx linear iterations at : 01:39:33 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 4.9804526E-05 1.2779236E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 01:39:34 3.399u 0.154s 0:03.92 90.3% 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 01:39:34 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2642 !!! WARNING: GLM 266 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.775797 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): 18.09900 78.24100 ymin,ymax (A): -11.52600 44.24500 zmin,zma (A): -7.594000 35.28800 x,y,z range (A): 60.14201 55.77100 42.88200 scale (grids/A): 1.775797 object centre (A): 48.17000 16.35950 13.84700 number of atom coordinates read : 2642 total number of charged atoms : 2495 net assigned charge : 4.906021 assigned positive charge : 398.4307 centred at (gu) : 84.68779 89.51272 89.09117 assigned negative charge : -393.5255 centred at (gu) : 85.56511 89.96339 89.59661 start vw surface at 0.2300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 65920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22230 grid for indexing accessible points = 1.400000 m= 21543 mr = 45684 m= 2907 mr = 15863 m= 96 mr = 1758 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2834 time to turn everything in is 0.5600000 number of dielectric boundary points 27141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19394 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) : 0.5919324 object centre at (A) : 48.17000 16.35950 13.84700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0716393E-02 3.7142169E-04 midg,1,midg; midg,igrid,midg 2.7457219E-02 -2.1003218E-02 1,midg,midg; igrid,midg,midg 5.6586098E-03 -1.4961467E-02 gauss-seidel spectral radius is 0.9984320 estimated iterations to convergence 200 setup time was (sec) 0.8400000 now iterating at: 01:39:35 rms-change max change #iterations 3.692822 186.6981 at 10iterations 1.638273 63.37010 at 20iterations 0.7255898 25.73556 at 30iterations 0.3211332 11.81189 at 40iterations 0.1426163 4.747192 at 50iterations 6.3394807E-02 2.436785 at 60iterations 2.8262934E-02 1.034895 at 70iterations 1.2652974E-02 0.4706879 at 80iterations 5.7299333E-03 0.1887760 at 90iterations 2.6706252E-03 9.6920013E-02 at 100iterations 1.2914082E-03 5.0148010E-02 at 110iterations 6.6033873E-04 2.9541969E-02 at 120iterations finished qdiffx linear iterations at : 01:39:41 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 6.6033873E-04 2.9541969E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 01:39:42 7.622u 0.193s 0:08.14 95.9% 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 01:39:42 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2642 !!! WARNING: GLM 266 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: 2.663696 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): 18.09900 78.24100 ymin,ymax (A): -11.52600 44.24500 zmin,zma (A): -7.594000 35.28800 x,y,z range (A): 60.14201 55.77100 42.88200 scale (grids/A): 2.663696 object centre (A): 48.17000 16.35950 13.84700 number of atom coordinates read : 2642 total number of charged atoms : 2495 net assigned charge : 4.906021 assigned positive charge : 398.4307 centred at (gu) : 82.03156 89.26900 88.63650 assigned negative charge : -393.5255 centred at (gu) : 83.34767 89.94493 89.39481 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 153020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22230 grid for indexing accessible points = 1.400000 m= 72627 mr = 111261 m= 23432 mr = 59207 m= 4961 mr = 18728 m= 514 mr = 3763 m= 12 mr = 304 m= 0 mr = 2 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 9289 time to turn everything in is 1.210000 number of dielectric boundary points 61301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19955 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) : 1.775797 object centre at (A) : 48.17000 16.35950 13.84700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2165028 1.1239505E-02 midg,1,midg; midg,igrid,midg 0.3360418 -0.4303493 1,midg,midg; igrid,midg,midg 1.9368581E-02 -2.0306319E-02 gauss-seidel spectral radius is 0.9991991 estimated iterations to convergence 279 setup time was (sec) 1.540000 now iterating at: 01:39:44 rms-change max change #iterations 8.956077 252.7458 at 10iterations 5.079041 116.4550 at 20iterations 2.861586 62.88317 at 30iterations 1.608605 31.32407 at 40iterations 0.9044378 19.13573 at 50iterations 0.5090390 10.81752 at 60iterations 0.2846794 5.671394 at 70iterations 0.1599145 3.666252 at 80iterations 8.9795962E-02 1.843063 at 90iterations 5.0566513E-02 1.025453 at 100iterations 2.8482476E-02 0.5326133 at 110iterations 1.6023340E-02 0.3329334 at 120iterations 9.0737157E-03 0.1944809 at 130iterations 5.1846979E-03 0.1053352 at 140iterations 3.0139131E-03 6.7550659E-02 at 150iterations 1.7888786E-03 4.4658661E-02 at 160iterations 1.1058312E-03 2.7759552E-02 at 170iterations 7.1529258E-04 1.9760132E-02 at 180iterations finished qdiffx linear iterations at : 01:39:55 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 7.1529258E-04 1.9760132E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 01:39:55 12.843u 0.237s 0:13.48 96.9% 0+0k 0+0io 0pf+0w