Sat Oct 8 17:56:31 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 Sat Oct 8 2011 at 17:56:31 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3549 !!! WARNING: GLM 79 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5506318 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): -2.811000 61.84200 ymin,ymax (A): -24.84300 29.62000 zmin,zma (A): -21.03400 32.51700 x,y,z range (A): 64.65300 54.46300 53.55100 scale (grids/A): 0.5506318 object centre (A): 29.51550 2.388500 5.741499 number of atom coordinates read : 3549 total number of charged atoms : 3398 net assigned charge : -2.593996 assigned positive charge : 536.8809 centred at (gu) : 88.11431 88.51806 91.28919 assigned negative charge : -539.4768 centred at (gu) : 88.15540 88.47514 91.36917 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6989 nv = 96 ne = 84 npr = 71418 no. pairs analyzed = 71418 no. exposed pairs = 4578 no. arc points = 31634 no. surface atoms = 1536 nbur = 2013 mkacc time = 0.1500000 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 = 1.540000 m= 283 mr = 3643 m= 0 mr = 16 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3613 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3165 ## 400 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9124 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1186315E-10 -1.3085304E-09 midg,1,midg; midg,igrid,midg -8.5438895E-10 1.5247162E-10 1,midg,midg; igrid,midg,midg 3.3894951E-10 -3.6278730E-10 gauss-seidel spectral radius is 0.9830344 estimated iterations to convergence 63 setup time was (sec) 0.6200000 now iterating at: 17:56:32 rms-change max change #iterations 8.7221593E-02 14.24214 at 10iterations 6.0756002E-03 0.9050255 at 20iterations 5.7576975E-04 0.1031361 at 30iterations 1.4912116E-04 2.9072762E-02 at 40iterations 5.5907032E-05 1.1689186E-02 at 50iterations finished qdiffx linear iterations at : 17:56:35 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 5.5907032E-05 1.1689186E-02 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 17:56:35 3.665u 0.247s 0:04.18 93.3% 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 Sat Oct 8 2011 at 17:56:35 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3549 !!! WARNING: GLM 79 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.651896 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): -2.811000 61.84200 ymin,ymax (A): -24.84300 29.62000 zmin,zma (A): -21.03400 32.51700 x,y,z range (A): 64.65300 54.46300 53.55100 scale (grids/A): 1.651896 object centre (A): 29.51550 2.388500 5.741499 number of atom coordinates read : 3549 total number of charged atoms : 3398 net assigned charge : -2.593996 assigned positive charge : 536.8809 centred at (gu) : 84.34175 85.55289 93.86659 assigned negative charge : -539.4768 centred at (gu) : 84.46572 85.42512 94.10686 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77324 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31634 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25417 mr = 52926 m= 2909 mr = 17734 m= 85 mr = 1458 m= 0 mr = 11 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 33606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 360 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 26092 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) : 0.5506318 object centre at (A) : 29.51550 2.388500 5.741499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1934887E-03 7.9142558E-04 midg,1,midg; midg,igrid,midg -1.0773520E-02 5.8409444E-04 1,midg,midg; igrid,midg,midg -2.5750252E-03 6.4369924E-03 gauss-seidel spectral radius is 0.9982759 estimated iterations to convergence 191 setup time was (sec) 0.8800000 now iterating at: 17:56:36 rms-change max change #iterations 3.803273 159.9206 at 10iterations 1.613809 50.67614 at 20iterations 0.6901964 27.68770 at 30iterations 0.2938986 10.31701 at 40iterations 0.1253040 3.973425 at 50iterations 5.3595100E-02 2.047936 at 60iterations 2.2859981E-02 0.7709374 at 70iterations 9.7809229E-03 0.3211427 at 80iterations 4.2107659E-03 0.1435242 at 90iterations 1.8383141E-03 5.8696747E-02 at 100iterations 8.3164626E-04 3.1278610E-02 at 110iterations 4.0794397E-04 1.8094063E-02 at 120iterations finished qdiffx linear iterations at : 17:56:43 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 4.0794397E-04 1.8094063E-02 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.330000 DelPhi exited at 17:56:44 8.331u 0.288s 0:08.99 95.7% 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 Sat Oct 8 2011 at 17:56:44 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3549 !!! WARNING: GLM 79 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.477843 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): -2.811000 61.84200 ymin,ymax (A): -24.84300 29.62000 zmin,zma (A): -21.03400 32.51700 x,y,z range (A): 64.65300 54.46300 53.55100 scale (grids/A): 2.477843 object centre (A): 29.51550 2.388500 5.741499 number of atom coordinates read : 3549 total number of charged atoms : 3398 net assigned charge : -2.593996 assigned positive charge : 536.8809 centred at (gu) : 81.51231 83.32907 95.79971 assigned negative charge : -539.4768 centred at (gu) : 81.69835 83.13760 96.16032 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 179052 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31634 grid for indexing accessible points = 1.400000 m= 86632 mr = 129273 m= 26579 mr = 68606 m= 4563 mr = 20206 m= 379 mr = 3064 m= 6 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 75898 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 27156 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) : 1.651896 object centre at (A) : 29.51550 2.388500 5.741499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1003782 7.7679977E-02 midg,1,midg; midg,igrid,midg -0.1361727 6.8536866E-03 1,midg,midg; igrid,midg,midg 9.8347448E-02 0.1376463 gauss-seidel spectral radius is 0.9991731 estimated iterations to convergence 275 setup time was (sec) 1.710000 now iterating at: 17:56:46 rms-change max change #iterations 9.768924 308.6295 at 10iterations 5.574540 131.3312 at 20iterations 3.172265 70.03897 at 30iterations 1.795786 36.13660 at 40iterations 1.011380 24.51111 at 50iterations 0.5682696 12.08063 at 60iterations 0.3188962 6.689917 at 70iterations 0.1781805 3.804001 at 80iterations 0.1000459 1.932833 at 90iterations 5.5753857E-02 1.170783 at 100iterations 3.1240340E-02 0.6042099 at 110iterations 1.7400308E-02 0.3345113 at 120iterations 9.7082714E-03 0.1754990 at 130iterations 5.4134140E-03 0.1111329 at 140iterations 3.0201732E-03 5.4947376E-02 at 150iterations 1.6900896E-03 3.4233093E-02 at 160iterations 9.4832596E-04 1.9195557E-02 at 170iterations 5.3696067E-04 1.1260986E-02 at 180iterations finished qdiffx linear iterations at : 17:56:58 total time elapsed so far: 13.80000 # loops : 180 mean,max change (kT/e) : 5.3696067E-04 1.1260986E-02 energy calculations done at 13.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.96000 DelPhi exited at 17:56:59 13.964u 0.302s 0:14.55 98.0% 0+0k 0+0io 0pf+0w