Sun Oct 9 21:30:52 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 Sun Oct 9 2011 at 21:30:52 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3283 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: CYS 258 has a net charge of 0.5000 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: 0.6434820 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): -20.84100 34.48300 ymin,ymax (A): -4.386000 49.49400 zmin,zma (A): -20.04200 32.03800 x,y,z range (A): 55.32400 53.88000 52.08000 scale (grids/A): 0.6434820 object centre (A): 6.821001 22.55400 5.997999 number of atom coordinates read : 3283 total number of charged atoms : 3154 net assigned charge : 6.025018 assigned positive charge : 503.4795 centred at (gu) : 90.60323 91.04807 89.52512 assigned negative charge : -497.4560 centred at (gu) : 90.53107 91.08329 89.50645 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9282 nv = 96 ne = 84 npr = 63421 no. pairs analyzed = 63421 no. exposed pairs = 4391 no. arc points = 31771 no. surface atoms = 1449 nbur = 1834 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 537 mr = 4894 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.3500000 number of dielectric boundary points 4878 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3083 ## 301 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 11148 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2739881E-09 1.1543744E-08 midg,1,midg; midg,igrid,midg 1.2408913E-08 4.7292534E-09 1,midg,midg; igrid,midg,midg -1.9134647E-09 2.4363288E-08 gauss-seidel spectral radius is 0.9875590 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 21:30:53 rms-change max change #iterations 0.1738123 26.05492 at 10iterations 1.7132061E-02 2.115783 at 20iterations 1.7279807E-03 0.2545462 at 30iterations 1.8143828E-04 2.3124695E-02 at 40iterations 2.2954955E-05 2.5024414E-03 at 50iterations finished qdiffx linear iterations at : 21:30:55 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.2954955E-05 2.5024414E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 21:30:56 3.418u 0.160s 0:03.89 91.7% 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 Sun Oct 9 2011 at 21:30:56 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3283 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: CYS 258 has a net charge of 0.5000 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: 1.930446 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): -20.84100 34.48300 ymin,ymax (A): -4.386000 49.49400 zmin,zma (A): -20.04200 32.03800 x,y,z range (A): 55.32400 53.88000 52.08000 scale (grids/A): 1.930446 object centre (A): 6.821001 22.55400 5.997999 number of atom coordinates read : 3283 total number of charged atoms : 3154 net assigned charge : 6.025018 assigned positive charge : 503.4795 centred at (gu) : 91.80895 93.14328 88.57458 assigned negative charge : -497.4560 centred at (gu) : 91.59286 93.24949 88.51895 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 99662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31771 grid for indexing accessible points = 1.400000 m= 35407 mr = 67241 m= 5738 mr = 25076 m= 423 mr = 3389 m= 10 mr = 180 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 3330 time to turn everything in is 0.7200000 number of dielectric boundary points 45354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 24828 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) : 0.6434820 object centre at (A) : 6.821001 22.55400 5.997999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7049209E-03 1.2238235E-02 midg,1,midg; midg,igrid,midg 2.5107764E-02 7.2612591E-02 1,midg,midg; igrid,midg,midg 1.4115568E-02 1.6891833E-02 gauss-seidel spectral radius is 0.9987538 estimated iterations to convergence 224 setup time was (sec) 1.010000 now iterating at: 21:30:57 rms-change max change #iterations 5.058086 171.6958 at 10iterations 2.436311 72.42785 at 20iterations 1.182275 38.12257 at 30iterations 0.5682985 15.99917 at 40iterations 0.2754927 8.283222 at 50iterations 0.1326946 3.540552 at 60iterations 6.4255178E-02 1.889834 at 70iterations 3.1043956E-02 0.9610724 at 80iterations 1.5040174E-02 0.4120979 at 90iterations 7.2708763E-03 0.1992242 at 100iterations 3.5205910E-03 9.5031261E-02 at 110iterations 1.7017309E-03 5.2515984E-02 at 120iterations finished qdiffx linear iterations at : 21:31:04 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.7017309E-03 5.2515984E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 21:31:04 7.789u 0.184s 0:08.24 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 21:31:04 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3283 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: CYS 258 has a net charge of 0.5000 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: 2.895669 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): -20.84100 34.48300 ymin,ymax (A): -4.386000 49.49400 zmin,zma (A): -20.04200 32.03800 x,y,z range (A): 55.32400 53.88000 52.08000 scale (grids/A): 2.895669 object centre (A): 6.821001 22.55400 5.997999 number of atom coordinates read : 3283 total number of charged atoms : 3154 net assigned charge : 6.025018 assigned positive charge : 503.4795 centred at (gu) : 92.71317 94.71461 87.86172 assigned negative charge : -497.4560 centred at (gu) : 92.38913 94.87411 87.77832 start vw surface at 0.1700000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 230217 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31771 grid for indexing accessible points = 1.400000 m= 114240 mr = 163552 m= 40972 mr = 91556 m= 10157 mr = 31625 m= 1707 mr = 7314 m= 143 mr = 1172 m= 5 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 11820 time to turn everything in is 1.840000 number of dielectric boundary points 102146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 25232 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) : 1.930446 object centre at (A) : 6.821001 22.55400 5.997999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1944053 0.1535905 midg,1,midg; midg,igrid,midg 0.2053813 0.6716145 1,midg,midg; igrid,midg,midg 0.3075889 0.1054910 gauss-seidel spectral radius is 0.9993192 estimated iterations to convergence 302 setup time was (sec) 2.150000 now iterating at: 21:31:06 rms-change max change #iterations 11.88000 341.2439 at 10iterations 7.210071 165.4963 at 20iterations 4.365304 103.4437 at 30iterations 2.614611 52.17156 at 40iterations 1.566107 31.62637 at 50iterations 0.9336641 15.61896 at 60iterations 0.5544413 10.64859 at 70iterations 0.3295834 5.895596 at 80iterations 0.1952523 3.377953 at 90iterations 0.1153902 1.978493 at 100iterations 6.8271756E-02 1.101208 at 110iterations 4.0357362E-02 0.7803802 at 120iterations 2.3791216E-02 0.4387531 at 130iterations 1.4019089E-02 0.2258759 at 140iterations 8.2804319E-03 0.1393104 at 150iterations 4.8803170E-03 8.4710598E-02 at 160iterations 2.8778547E-03 4.4509888E-02 at 170iterations 1.6956270E-03 2.6626110E-02 at 180iterations finished qdiffx linear iterations at : 21:31:17 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 1.6956270E-03 2.6626110E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.14000 DelPhi exited at 21:31:18 13.139u 0.202s 0:13.62 97.8% 0+0k 0+0io 0pf+0w