Sun Oct 9 13:11:18 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 13:11:18 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 = 2375 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: 0.6938489 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): -6.716000 44.59200 ymin,ymax (A): -14.08600 36.90000 zmin,zma (A): 2.244000 44.94600 x,y,z range (A): 51.30800 50.98600 42.70200 scale (grids/A): 0.6938489 object centre (A): 18.93800 11.40700 23.59500 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500020 assigned positive charge : 361.0370 centred at (gu) : 89.65307 91.32008 90.77700 assigned negative charge : -357.5376 centred at (gu) : 89.69174 91.48456 90.79935 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7775 nv = 96 ne = 84 npr = 47366 no. pairs analyzed = 47366 no. exposed pairs = 3010 no. arc points = 21123 no. surface atoms = 1012 nbur = 1363 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 487 mr = 4248 m= 3 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3928 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1984 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8719 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7156675E-08 1.5051210E-08 midg,1,midg; midg,igrid,midg 6.8810948E-08 -6.2135285E-08 1,midg,midg; igrid,midg,midg 4.1022115E-08 5.8848224E-09 gauss-seidel spectral radius is 0.9892092 estimated iterations to convergence 78 setup time was (sec) 0.4600000 now iterating at: 13:11:19 rms-change max change #iterations 0.1944970 26.41405 at 10iterations 2.3598853E-02 2.991711 at 20iterations 3.0253683E-03 0.5082436 at 30iterations 5.2429718E-04 7.6000214E-02 at 40iterations 1.3442918E-04 2.0931244E-02 at 50iterations finished qdiffx linear iterations at : 13:11:21 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 1.3442918E-04 2.0931244E-02 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 13:11:22 3.041u 0.157s 0:03.49 91.4% 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 13:11:22 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 = 2375 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: 2.081547 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): -6.716000 44.59200 ymin,ymax (A): -14.08600 36.90000 zmin,zma (A): 2.244000 44.94600 x,y,z range (A): 51.30800 50.98600 42.70200 scale (grids/A): 2.081547 object centre (A): 18.93800 11.40700 23.59500 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500020 assigned positive charge : 361.0370 centred at (gu) : 88.95878 93.95973 92.33065 assigned negative charge : -357.5376 centred at (gu) : 89.07498 94.45356 92.39777 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 82808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21123 grid for indexing accessible points = 1.400000 m= 31394 mr = 57391 m= 5434 mr = 23224 m= 496 mr = 3391 m= 14 mr = 251 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 35889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17714 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) : 0.6938489 object centre at (A) : 18.93800 11.40700 23.59500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7929103E-02 1.1605381E-02 midg,1,midg; midg,igrid,midg 1.5855184E-02 -4.2970531E-02 1,midg,midg; igrid,midg,midg 5.7762798E-02 -1.4063876E-02 gauss-seidel spectral radius is 0.9988295 estimated iterations to convergence 231 setup time was (sec) 0.8300000 now iterating at: 13:11:23 rms-change max change #iterations 4.857000 211.3712 at 10iterations 2.385454 79.88565 at 20iterations 1.177704 37.29787 at 30iterations 0.5841973 18.60099 at 40iterations 0.2892378 9.084303 at 50iterations 0.1434287 4.696214 at 60iterations 7.1570374E-02 2.045036 at 70iterations 3.5589810E-02 1.024046 at 80iterations 1.7659500E-02 0.5251808 at 90iterations 8.8940654E-03 0.2657890 at 100iterations 4.5159371E-03 0.1352482 at 110iterations 2.3538589E-03 7.1452141E-02 at 120iterations finished qdiffx linear iterations at : 13:11:29 total time elapsed so far: 7.150000 # loops : 120 mean,max change (kT/e) : 2.3538589E-03 7.1452141E-02 energy calculations done at 7.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 13:11:29 7.350u 0.161s 0:07.77 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 13:11:29 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 = 2375 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: 3.122320 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): -6.716000 44.59200 ymin,ymax (A): -14.08600 36.90000 zmin,zma (A): 2.244000 44.94600 x,y,z range (A): 51.30800 50.98600 42.70200 scale (grids/A): 3.122320 object centre (A): 18.93800 11.40700 23.59500 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500020 assigned positive charge : 361.0370 centred at (gu) : 88.43822 95.93934 93.49591 assigned negative charge : -357.5376 centred at (gu) : 88.61246 96.68038 93.59669 start vw surface at 0.1300000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 190790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21123 grid for indexing accessible points = 1.400000 m= 99850 mr = 138562 m= 37848 mr = 81637 m= 9865 mr = 30433 m= 1894 mr = 7423 m= 266 mr = 1384 m= 4 mr = 182 m= 0 mr = 2 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.780000 number of dielectric boundary points 80894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 17867 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) : 2.081547 object centre at (A) : 18.93800 11.40700 23.59500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3569436 -8.4396882E-04 midg,1,midg; midg,igrid,midg 0.2762434 -0.4446285 1,midg,midg; igrid,midg,midg 0.6462156 -0.4280729 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.050000 now iterating at: 13:11:32 rms-change max change #iterations 10.87889 497.1980 at 10iterations 6.465195 134.3511 at 20iterations 3.835377 75.35353 at 30iterations 2.269132 42.60209 at 40iterations 1.343877 22.78319 at 50iterations 0.7900836 14.16339 at 60iterations 0.4647746 7.754551 at 70iterations 0.2731173 4.456589 at 80iterations 0.1605153 2.668816 at 90iterations 9.4319291E-02 1.627456 at 100iterations 5.5300605E-02 0.9416776 at 110iterations 3.2681689E-02 0.5557933 at 120iterations 1.9328520E-02 0.3621216 at 130iterations 1.1580837E-02 0.2112942 at 140iterations 7.0592514E-03 0.1493988 at 150iterations 4.4642957E-03 9.3603134E-02 at 160iterations 2.9619380E-03 6.0894012E-02 at 170iterations 2.0898602E-03 4.4475555E-02 at 180iterations finished qdiffx linear iterations at : 13:11:41 total time elapsed so far: 11.42000 # loops : 180 mean,max change (kT/e) : 2.0898602E-03 4.4475555E-02 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 13:11:42 11.598u 0.184s 0:12.05 97.6% 0+0k 0+0io 0pf+0w