Sat Oct 15 12:06:39 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 Sat Oct 15 2011 at 12:06:39 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3293 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5720621 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): -15.88100 40.22800 ymin,ymax (A): 16.91800 76.95700 zmin,zma (A): 25.37600 87.60700 x,y,z range (A): 56.10900 60.03900 62.23100 scale (grids/A): 0.5720621 object centre (A): 12.17350 46.93750 56.49150 number of atom coordinates read : 3293 total number of charged atoms : 3152 net assigned charge : 12.22603 assigned positive charge : 485.4918 centred at (gu) : 89.92366 90.06591 90.76302 assigned negative charge : -473.2674 centred at (gu) : 89.79337 90.11047 90.93362 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7416 nv = 96 ne = 84 npr = 64369 no. pairs analyzed = 64369 no. exposed pairs = 4261 no. arc points = 30966 no. surface atoms = 1420 nbur = 1873 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 334 mr = 3842 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2400000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3100 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9292 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2210702E-09 -1.3134758E-09 midg,1,midg; midg,igrid,midg 2.8046818E-09 1.2672673E-09 1,midg,midg; igrid,midg,midg -3.3044109E-10 4.2768229E-09 gauss-seidel spectral radius is 0.9842693 estimated iterations to convergence 66 setup time was (sec) 0.4400000 now iterating at: 12:06:40 rms-change max change #iterations 9.7573407E-02 14.89891 at 10iterations 7.2729383E-03 1.189304 at 20iterations 5.6762999E-04 9.4687462E-02 at 30iterations 4.8378632E-05 6.5155029E-03 at 40iterations 5.4802194E-06 6.9856644E-04 at 50iterations finished qdiffx linear iterations at : 12:06:43 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 5.4802194E-06 6.9856644E-04 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 12:06:43 3.837u 0.238s 0:04.34 93.5% 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 Sat Oct 15 2011 at 12:06:44 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3293 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.716186 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): -15.88100 40.22800 ymin,ymax (A): 16.91800 76.95700 zmin,zma (A): 25.37600 87.60700 x,y,z range (A): 56.10900 60.03900 62.23100 scale (grids/A): 1.716186 object centre (A): 12.17350 46.93750 56.49150 number of atom coordinates read : 3293 total number of charged atoms : 3152 net assigned charge : 12.22603 assigned positive charge : 485.4918 centred at (gu) : 89.76986 90.19655 92.28825 assigned negative charge : -473.2674 centred at (gu) : 89.37991 90.33118 92.80046 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 81261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30966 grid for indexing accessible points = 1.400000 m= 26191 mr = 54860 m= 3214 mr = 18385 m= 135 mr = 1731 m= 0 mr = 37 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2177 time to turn everything in is 0.4400000 number of dielectric boundary points 35788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 24342 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) : 0.5720621 object centre at (A) : 12.17350 46.93750 56.49150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3995231E-02 7.8831203E-03 midg,1,midg; midg,igrid,midg 3.5836149E-02 1.6563548E-02 1,midg,midg; igrid,midg,midg -6.8476740E-03 1.5596617E-02 gauss-seidel spectral radius is 0.9984103 estimated iterations to convergence 199 setup time was (sec) 0.7700000 now iterating at: 12:06:45 rms-change max change #iterations 3.857471 160.1452 at 10iterations 1.690445 63.02283 at 20iterations 0.7412098 22.93918 at 30iterations 0.3262287 10.53847 at 40iterations 0.1441954 4.446433 at 50iterations 6.3407823E-02 1.994476 at 60iterations 2.8002795E-02 0.9293051 at 70iterations 1.2348444E-02 0.3876877 at 80iterations 5.4404479E-03 0.1716895 at 90iterations 2.3906080E-03 7.6721191E-02 at 100iterations 1.0590315E-03 3.8185120E-02 at 110iterations 4.6582622E-04 1.5586853E-02 at 120iterations finished qdiffx linear iterations at : 12:06:54 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 4.6582622E-04 1.5586853E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.800000 DelPhi exited at 12:06:54 9.800u 0.352s 0:10.45 97.1% 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 Sat Oct 15 2011 at 12:06:54 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3293 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.574280 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): -15.88100 40.22800 ymin,ymax (A): 16.91800 76.95700 zmin,zma (A): 25.37600 87.60700 x,y,z range (A): 56.10900 60.03900 62.23100 scale (grids/A): 2.574280 object centre (A): 12.17350 46.93750 56.49150 number of atom coordinates read : 3293 total number of charged atoms : 3152 net assigned charge : 12.22603 assigned positive charge : 485.4918 centred at (gu) : 89.65469 90.29463 93.43203 assigned negative charge : -473.2674 centred at (gu) : 89.06989 90.49675 94.20067 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 188486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30966 grid for indexing accessible points = 1.400000 m= 88945 mr = 134350 m= 27335 mr = 70639 m= 5240 mr = 20927 m= 544 mr = 3615 m= 15 mr = 308 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 7274 time to turn everything in is 1.050000 number of dielectric boundary points 80726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 25173 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) : 1.716186 object centre at (A) : 12.17350 46.93750 56.49150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6885041 8.5013777E-02 midg,1,midg; midg,igrid,midg 0.5964844 0.3678911 1,midg,midg; igrid,midg,midg -4.1025836E-02 0.2206882 gauss-seidel spectral radius is 0.9992211 estimated iterations to convergence 283 setup time was (sec) 1.350000 now iterating at: 12:06:56 rms-change max change #iterations 9.787616 330.9875 at 10iterations 5.692421 142.7106 at 20iterations 3.287179 77.73563 at 30iterations 1.885983 39.63332 at 40iterations 1.080370 21.73224 at 50iterations 0.6153435 12.76560 at 60iterations 0.3501662 6.708726 at 70iterations 0.1991558 3.882502 at 80iterations 0.1132785 2.082512 at 90iterations 6.4289309E-02 1.311485 at 100iterations 3.6361814E-02 0.6592712 at 110iterations 2.0638697E-02 0.4265661 at 120iterations 1.1652726E-02 0.2078550 at 130iterations 6.6081439E-03 0.1277428 at 140iterations 3.7440262E-03 7.2892666E-02 at 150iterations 2.1219393E-03 4.1151047E-02 at 160iterations 1.1991623E-03 2.1965027E-02 at 170iterations 6.7896699E-04 1.1936188E-02 at 180iterations finished qdiffx linear iterations at : 12:07:10 total time elapsed so far: 15.31000 # loops : 180 mean,max change (kT/e) : 6.7896699E-04 1.1936188E-02 energy calculations done at 15.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.44000 DelPhi exited at 12:07:10 15.441u 0.329s 0:16.35 96.3% 0+0k 0+0io 0pf+0w