Mon Oct 10 19:36:35 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 Mon Oct 10 2011 at 19:36:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 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: 0.6135815 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): -12.48400 39.82700 ymin,ymax (A): -35.22600 22.79400 zmin,zma (A): 3.810000 61.44900 x,y,z range (A): 52.31100 58.02000 57.63900 scale (grids/A): 0.6135815 object centre (A): 13.67150 -6.216001 32.62950 number of atom coordinates read : 2700 total number of charged atoms : 2564 net assigned charge : 9.500033 assigned positive charge : 399.6616 centred at (gu) : 90.14949 93.14500 89.01158 assigned negative charge : -390.1628 centred at (gu) : 90.18662 93.20668 89.04218 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6850 nv = 96 ne = 84 npr = 52739 no. pairs analyzed = 52739 no. exposed pairs = 3810 no. arc points = 26882 no. surface atoms = 1275 nbur = 1425 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 410 mr = 3387 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2663 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8389 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8878008E-09 3.7585601E-09 midg,1,midg; midg,igrid,midg 4.9068363E-09 5.5299463E-09 1,midg,midg; igrid,midg,midg 8.0537674E-09 4.3994599E-09 gauss-seidel spectral radius is 0.9862676 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 19:36:36 rms-change max change #iterations 0.1174948 17.54796 at 10iterations 1.0770359E-02 1.678486 at 20iterations 1.0219471E-03 0.1448898 at 30iterations 1.1931227E-04 2.0713806E-02 at 40iterations 2.0542533E-05 3.8156509E-03 at 50iterations finished qdiffx linear iterations at : 19:36:39 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.0542533E-05 3.8156509E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 19:36:39 3.435u 0.195s 0:03.91 92.5% 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 Mon Oct 10 2011 at 19:36:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 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: 1.840744 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): -12.48400 39.82700 ymin,ymax (A): -35.22600 22.79400 zmin,zma (A): 3.810000 61.44900 x,y,z range (A): 52.31100 58.02000 57.63900 scale (grids/A): 1.840744 object centre (A): 13.67150 -6.216001 32.62950 number of atom coordinates read : 2700 total number of charged atoms : 2564 net assigned charge : 9.500033 assigned positive charge : 399.6616 centred at (gu) : 90.44785 99.43443 87.03401 assigned negative charge : -390.1628 centred at (gu) : 90.55984 99.62000 87.12672 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73418 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26882 grid for indexing accessible points = 1.400000 m= 25637 mr = 47512 m= 4392 mr = 17963 m= 287 mr = 2640 m= 5 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 196 time to turn everything in is 0.3800000 number of dielectric boundary points 35534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20063 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) : 0.6135815 object centre at (A) : 13.67150 -6.216001 32.62950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8319274E-03 1.2489960E-02 midg,1,midg; midg,igrid,midg 3.2813016E-02 5.3148575E-02 1,midg,midg; igrid,midg,midg 1.6856354E-02 2.6085997E-02 gauss-seidel spectral radius is 0.9985631 estimated iterations to convergence 209 setup time was (sec) 0.6000000 now iterating at: 19:36:40 rms-change max change #iterations 3.978259 166.5498 at 10iterations 1.826928 70.15614 at 20iterations 0.8385507 25.24277 at 30iterations 0.3839083 13.02426 at 40iterations 0.1759034 5.750809 at 50iterations 8.0876231E-02 2.519989 at 60iterations 3.7065685E-02 1.148556 at 70iterations 1.7056772E-02 0.5894318 at 80iterations 7.8311563E-03 0.2630558 at 90iterations 3.6109705E-03 0.1209831 at 100iterations 1.6576451E-03 5.4786682E-02 at 110iterations 7.7108829E-04 2.7043939E-02 at 120iterations finished qdiffx linear iterations at : 19:36:47 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 7.7108829E-04 2.7043939E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 19:36:47 7.972u 0.204s 0:08.46 96.5% 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 Mon Oct 10 2011 at 19:36:48 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 = 2700 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: 2.761117 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): -12.48400 39.82700 ymin,ymax (A): -35.22600 22.79400 zmin,zma (A): 3.810000 61.44900 x,y,z range (A): 52.31100 58.02000 57.63900 scale (grids/A): 2.761117 object centre (A): 13.67150 -6.216001 32.62950 number of atom coordinates read : 2700 total number of charged atoms : 2564 net assigned charge : 9.500033 assigned positive charge : 399.6616 centred at (gu) : 90.67141 104.1513 85.55090 assigned negative charge : -390.1628 centred at (gu) : 90.83968 104.4300 85.68992 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 169558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26882 grid for indexing accessible points = 1.400000 m= 81892 mr = 116557 m= 30658 mr = 64207 m= 7786 mr = 23833 m= 1146 mr = 5727 m= 76 mr = 729 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 685 time to turn everything in is 0.9600000 number of dielectric boundary points 80050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 20502 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) : 1.840744 object centre at (A) : 13.67150 -6.216001 32.62950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9384691E-03 0.1482962 midg,1,midg; midg,igrid,midg 0.3581095 0.9020289 1,midg,midg; igrid,midg,midg 0.1417193 0.3821996 gauss-seidel spectral radius is 0.9992568 estimated iterations to convergence 290 setup time was (sec) 1.210000 now iterating at: 19:36:49 rms-change max change #iterations 9.799771 338.5859 at 10iterations 5.813959 140.8192 at 20iterations 3.420524 69.68230 at 30iterations 1.995318 40.03221 at 40iterations 1.157427 22.63912 at 50iterations 0.6722810 13.03576 at 60iterations 0.3893410 8.435833 at 70iterations 0.2247849 4.639744 at 80iterations 0.1296399 2.632875 at 90iterations 7.4707873E-02 1.421774 at 100iterations 4.2947676E-02 0.7918339 at 110iterations 2.4713609E-02 0.5094795 at 120iterations 1.4225080E-02 0.2729836 at 130iterations 8.1838174E-03 0.1482782 at 140iterations 4.7227680E-03 9.8830223E-02 at 150iterations 2.7198319E-03 4.7574997E-02 at 160iterations 1.5809021E-03 2.9734612E-02 at 170iterations 9.2109811E-04 1.8071651E-02 at 180iterations finished qdiffx linear iterations at : 19:37:01 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 9.2109811E-04 1.8071651E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 19:37:01 12.896u 0.202s 0:13.53 96.7% 0+0k 0+0io 0pf+0w