Sat Oct 8 18:34:54 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 Sat Oct 8 2011 at 18:34:54 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! 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 : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 88.45907 89.30300 89.90370 assigned negative charge : -386.9045 centred at (gu) : 88.37026 89.36083 89.78457 start vw surface at 9.0000004E-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 = 0.1000000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.2000000 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 0.2700000 number of grid points assigned charge 8256 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2877588E-09 1.6557614E-08 midg,1,midg; midg,igrid,midg 1.2886417E-08 -4.8880972E-11 1,midg,midg; igrid,midg,midg -4.5766777E-09 1.0099907E-08 gauss-seidel spectral radius is 0.9870834 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 18:34:54 rms-change max change #iterations 0.1388907 22.45007 at 10iterations 1.3422189E-02 2.025780 at 20iterations 1.3107897E-03 0.1846962 at 30iterations 1.2846584E-04 1.8705368E-02 at 40iterations 1.2369203E-05 1.7919540E-03 at 50iterations finished qdiffx linear iterations at : 18:34:58 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 1.2369203E-05 1.7919540E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 18:34:58 3.650u 0.207s 0:04.13 93.2% 0+0k 0+0io 6pf+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 18:34:58 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! 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 : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 85.37693 87.90903 89.71055 assigned negative charge : -386.9045 centred at (gu) : 85.11055 88.08215 89.35336 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 = 0.1700000 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 19261 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 -1.6193999E-02 2.2633465E-02 midg,1,midg; midg,igrid,midg 1.3551517E-02 3.6891285E-04 1,midg,midg; igrid,midg,midg -7.2670385E-04 3.5969444E-02 gauss-seidel spectral radius is 0.9986219 estimated iterations to convergence 213 setup time was (sec) 0.6000000 now iterating at: 18:34:59 rms-change max change #iterations 4.179163 181.5779 at 10iterations 1.944777 63.86345 at 20iterations 0.9100673 27.91615 at 30iterations 0.4254084 14.02285 at 40iterations 0.1981332 6.517458 at 50iterations 9.2751309E-02 2.979431 at 60iterations 4.3206587E-02 1.348859 at 70iterations 2.0171583E-02 0.6735461 at 80iterations 9.4352672E-03 0.3052063 at 90iterations 4.4018743E-03 0.1441994 at 100iterations 2.0579149E-03 6.1217308E-02 at 110iterations 9.6114620E-04 3.3157349E-02 at 120iterations finished qdiffx linear iterations at : 18:35:07 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 9.6114620E-04 3.3157349E-02 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 18:35:07 8.445u 0.255s 0:09.01 96.4% 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 Sat Oct 8 2011 at 18:35:07 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! 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 : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 83.06518 86.86338 89.56579 assigned negative charge : -386.9045 centred at (gu) : 82.66566 87.12315 89.03008 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 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 = 0.5200000 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 1.070000 number of grid points assigned charge 19614 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 -6.4649962E-02 0.1678016 midg,1,midg; midg,igrid,midg 0.1749185 -1.2792864E-02 1,midg,midg; igrid,midg,midg 1.5797557E-02 0.4596889 gauss-seidel spectral radius is 0.9992480 estimated iterations to convergence 288 setup time was (sec) 1.240000 now iterating at: 18:35:08 rms-change max change #iterations 9.682550 437.5044 at 10iterations 5.550311 105.8325 at 20iterations 3.167393 65.76712 at 30iterations 1.809141 34.22412 at 40iterations 1.033378 18.14746 at 50iterations 0.5889699 10.30806 at 60iterations 0.3375355 6.287765 at 70iterations 0.1923901 3.306778 at 80iterations 0.1097794 1.979963 at 90iterations 6.2796682E-02 1.101286 at 100iterations 3.5765108E-02 0.6343422 at 110iterations 2.0423964E-02 0.3728237 at 120iterations 1.1675067E-02 0.2329311 at 130iterations 6.6682892E-03 0.1213179 at 140iterations 3.8085205E-03 6.6660404E-02 at 150iterations 2.1756561E-03 4.0172815E-02 at 160iterations 1.2442142E-03 2.2628784E-02 at 170iterations 7.1076769E-04 1.3885498E-02 at 180iterations finished qdiffx linear iterations at : 18:35:21 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 7.1076769E-04 1.3885498E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.49000 DelPhi exited at 18:35:21 13.496u 0.241s 0:14.04 97.7% 0+0k 0+0io 0pf+0w