Sat Oct 8 18:35:21 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 18:35:21 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6334294 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): -31.81100 17.41700 ymin,ymax (A): -23.19400 22.23400 zmin,zma (A): -12.08400 44.11800 x,y,z range (A): 49.22800 45.42800 56.20200 scale (grids/A): 0.6334294 object centre (A): -7.197001 -0.4800005 16.01700 number of atom coordinates read : 2586 total number of charged atoms : 2449 net assigned charge : 4.406008 assigned positive charge : 392.2440 centred at (gu) : 88.47250 89.30026 89.90578 assigned negative charge : -387.8386 centred at (gu) : 88.38757 89.35650 89.78551 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6852 nv = 96 ne = 84 npr = 53857 no. pairs analyzed = 53857 no. exposed pairs = 2940 no. arc points = 21057 no. surface atoms = 992 nbur = 1594 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 372 mr = 3939 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.1900000 number of dielectric boundary points 3225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2100 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8245 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.5526780E-09 1.6581412E-08 midg,1,midg; midg,igrid,midg 1.2593415E-08 -2.9325216E-11 1,midg,midg; igrid,midg,midg -4.2169011E-09 9.7918855E-09 gauss-seidel spectral radius is 0.9870834 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 18:35:22 rms-change max change #iterations 0.1404923 22.35895 at 10iterations 1.3576178E-02 2.039188 at 20iterations 1.3236137E-03 0.1864738 at 30iterations 1.2982548E-04 1.9176483E-02 at 40iterations 1.2493514E-05 1.7604828E-03 at 50iterations finished qdiffx linear iterations at : 18:35:25 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.2493514E-05 1.7604828E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 18:35:25 3.592u 0.210s 0:04.14 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 Sat Oct 8 2011 at 18:35:25 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.900288 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): -31.81100 17.41700 ymin,ymax (A): -23.19400 22.23400 zmin,zma (A): -12.08400 44.11800 x,y,z range (A): 49.22800 45.42800 56.20200 scale (grids/A): 1.900288 object centre (A): -7.197001 -0.4800005 16.01700 number of atom coordinates read : 2586 total number of charged atoms : 2449 net assigned charge : 4.406008 assigned positive charge : 392.2440 centred at (gu) : 85.41721 87.90080 89.71677 assigned negative charge : -387.8386 centred at (gu) : 85.16249 88.06919 89.35622 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21057 grid for indexing accessible points = 1.400000 m= 26743 mr = 52273 m= 4170 mr = 20438 m= 249 mr = 2786 m= 4 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3237 time to turn everything in is 0.3600000 number of dielectric boundary points 29495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19229 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) : 0.6334294 object centre at (A) : -7.197001 -0.4800005 16.01700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6474264E-02 2.2771500E-02 midg,1,midg; midg,igrid,midg 1.3347078E-02 4.2876982E-04 1,midg,midg; igrid,midg,midg -5.8885012E-04 3.5148837E-02 gauss-seidel spectral radius is 0.9986219 estimated iterations to convergence 213 setup time was (sec) 0.6000000 now iterating at: 18:35:26 rms-change max change #iterations 4.197017 181.5779 at 10iterations 1.953089 63.85629 at 20iterations 0.9137459 28.32968 at 30iterations 0.4271307 14.13653 at 40iterations 0.1989655 6.677949 at 50iterations 9.3128957E-02 2.979584 at 60iterations 4.3368530E-02 1.342290 at 70iterations 2.0255214E-02 0.6977289 at 80iterations 9.4735827E-03 0.3017235 at 90iterations 4.4194888E-03 0.1430683 at 100iterations 2.0663594E-03 6.1520100E-02 at 110iterations 9.6535584E-04 3.2562256E-02 at 120iterations finished qdiffx linear iterations at : 18:35:49 total time elapsed so far: 8.400000 # loops : 120 mean,max change (kT/e) : 9.6535584E-04 3.2562256E-02 energy calculations done at 8.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.540000 DelPhi exited at 18:35:50 8.540u 0.240s 0:24.44 35.9% 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 18:35:50 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.850432 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): -31.81100 17.41700 ymin,ymax (A): -23.19400 22.23400 zmin,zma (A): -12.08400 44.11800 x,y,z range (A): 49.22800 45.42800 56.20200 scale (grids/A): 2.850432 object centre (A): -7.197001 -0.4800005 16.01700 number of atom coordinates read : 2586 total number of charged atoms : 2449 net assigned charge : 4.406008 assigned positive charge : 392.2440 centred at (gu) : 83.12560 86.85104 89.57510 assigned negative charge : -387.8386 centred at (gu) : 82.74359 87.10371 89.03435 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 170927 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21057 grid for indexing accessible points = 1.400000 m= 87645 mr = 126103 m= 31272 mr = 73353 m= 7498 mr = 25803 m= 1082 mr = 5909 m= 66 mr = 777 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 10877 time to turn everything in is 0.9800000 number of dielectric boundary points 66513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 19582 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) : 1.900288 object centre at (A) : -7.197001 -0.4800005 16.01700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7855120E-02 0.1697640 midg,1,midg; midg,igrid,midg 0.1731593 -1.2083930E-02 1,midg,midg; igrid,midg,midg 1.7329138E-02 0.4506731 gauss-seidel spectral radius is 0.9992480 estimated iterations to convergence 288 setup time was (sec) 1.260000 now iterating at: 18:35:51 rms-change max change #iterations 9.719061 437.5044 at 10iterations 5.571785 105.8326 at 20iterations 3.179933 65.76517 at 30iterations 1.816183 34.96019 at 40iterations 1.037409 18.29295 at 50iterations 0.5913454 10.31720 at 60iterations 0.3388454 6.328908 at 70iterations 0.1930916 3.397984 at 80iterations 0.1101822 1.991232 at 90iterations 6.3012831E-02 1.112764 at 100iterations 3.5893399E-02 0.6531830 at 110iterations 2.0499745E-02 0.3801250 at 120iterations 1.1719285E-02 0.2338791 at 130iterations 6.6916733E-03 0.1252069 at 140iterations 3.8220221E-03 6.7324638E-02 at 150iterations 2.1838683E-03 3.9883375E-02 at 160iterations 1.2485477E-03 2.2644043E-02 at 170iterations 7.1335526E-04 1.4244080E-02 at 180iterations finished qdiffx linear iterations at : 18:36:04 total time elapsed so far: 13.89000 # loops : 180 mean,max change (kT/e) : 7.1335526E-04 1.4244080E-02 energy calculations done at 13.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.02000 DelPhi exited at 18:36:05 14.020u 0.266s 0:14.56 98.0% 0+0k 0+0io 0pf+0w