Sun Oct 9 19:56:07 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 19:56:08 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: 353 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5044136 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): 3.237000 67.98900 ymin,ymax (A): -8.816000 53.26900 zmin,zma (A): -2.231000 68.34600 x,y,z range (A): 64.75200 62.08500 70.57700 scale (grids/A): 0.5044136 object centre (A): 35.61300 22.22650 33.05750 number of atom coordinates read : 5505 total number of charged atoms : 5336 net assigned charge : 5.654033 assigned positive charge : 848.7448 centred at (gu) : 88.10273 89.32695 88.76079 assigned negative charge : -843.0970 centred at (gu) : 88.02014 89.36610 88.66245 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8846 nv = 96 ne = 84 npr = 112861 no. pairs analyzed = 112861 no. exposed pairs = 6311 no. arc points = 42833 no. surface atoms = 2159 nbur = 3346 mkacc time = 0.2000000 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 = 1.708000 m= 307 mr = 4938 m= 0 mr = 5 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4219 ## 594 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 11882 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3209841E-10 2.1038664E-10 midg,1,midg; midg,igrid,midg 1.8857649E-10 -2.0019056E-11 1,midg,midg; igrid,midg,midg -2.1605810E-10 1.5542825E-10 gauss-seidel spectral radius is 0.9799431 estimated iterations to convergence 58 setup time was (sec) 0.5500000 now iterating at: 19:56:08 rms-change max change #iterations 7.6244220E-02 11.64813 at 10iterations 9.8141376E-03 1.610836 at 20iterations 3.9761402E-03 0.7261887 at 30iterations 1.8230043E-03 0.3305969 at 40iterations 8.4987521E-04 0.1503448 at 50iterations finished qdiffx linear iterations at : 19:56:11 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 8.4987521E-04 0.1503448 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 19:56:12 3.583u 0.191s 0:04.05 93.0% 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 19:56:12 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: 353 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.513241 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): 3.237000 67.98900 ymin,ymax (A): -8.816000 53.26900 zmin,zma (A): -2.231000 68.34600 x,y,z range (A): 64.75200 62.08500 70.57700 scale (grids/A): 1.513241 object centre (A): 35.61300 22.22650 33.05750 number of atom coordinates read : 5505 total number of charged atoms : 5336 net assigned charge : 5.654033 assigned positive charge : 848.7448 centred at (gu) : 84.30676 87.97904 86.28063 assigned negative charge : -843.0970 centred at (gu) : 84.06034 88.09790 85.98717 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 101278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42833 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 30720 mr = 73200 m= 2729 mr = 21279 m= 50 mr = 1181 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 267 time to turn everything in is 0.4900000 number of dielectric boundary points 39117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 557 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 39827 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) : 0.5044136 object centre at (A) : 35.61300 22.22650 33.05750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4855302E-02 1.9612342E-02 midg,1,midg; midg,igrid,midg 1.2448080E-02 4.3733739E-03 1,midg,midg; igrid,midg,midg -7.9011889E-03 5.5653434E-03 gauss-seidel spectral radius is 0.9981050 estimated iterations to convergence 183 setup time was (sec) 0.7100000 now iterating at: 19:56:12 rms-change max change #iterations 4.118049 166.3356 at 10iterations 1.689681 54.24506 at 20iterations 0.6924189 20.31990 at 30iterations 0.2838317 9.909868 at 40iterations 0.1176645 3.626247 at 50iterations 4.9706645E-02 1.513168 at 60iterations 2.1982400E-02 0.7592888 at 70iterations 1.0894582E-02 0.3671570 at 80iterations 6.3797841E-03 0.2248039 at 90iterations 4.2464901E-03 0.1455574 at 100iterations 3.0429144E-03 0.1066933 at 110iterations 2.2377414E-03 7.2311401E-02 at 120iterations finished qdiffx linear iterations at : 19:56:20 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 2.2377414E-03 7.2311401E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 19:56:20 8.024u 0.197s 0:08.58 95.6% 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 19:56:20 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: 353 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.269861 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): 3.237000 67.98900 ymin,ymax (A): -8.816000 53.26900 zmin,zma (A): -2.231000 68.34600 x,y,z range (A): 64.75200 62.08500 70.57700 scale (grids/A): 2.269861 object centre (A): 35.61300 22.22650 33.05750 number of atom coordinates read : 5505 total number of charged atoms : 5336 net assigned charge : 5.654033 assigned positive charge : 848.7448 centred at (gu) : 81.45985 86.96825 84.42069 assigned negative charge : -843.0970 centred at (gu) : 81.09048 87.14681 83.98064 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 236365 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42833 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 110225 mr = 179064 m= 28721 mr = 88520 m= 3859 mr = 21195 m= 199 mr = 2348 m= 2 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 822 time to turn everything in is 1.200000 number of dielectric boundary points 88148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 42522 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) : 1.513241 object centre at (A) : 35.61300 22.22650 33.05750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3441897 0.6394389 midg,1,midg; midg,igrid,midg 0.2177049 5.1629700E-02 1,midg,midg; igrid,midg,midg -0.2477483 8.0570534E-02 gauss-seidel spectral radius is 0.9991603 estimated iterations to convergence 273 setup time was (sec) 1.460000 now iterating at: 19:56:22 rms-change max change #iterations 10.96141 251.1534 at 10iterations 6.231859 121.0568 at 20iterations 3.519367 68.11758 at 30iterations 1.977271 37.67366 at 40iterations 1.106506 19.83243 at 50iterations 0.6178191 12.37754 at 60iterations 0.3459936 6.708696 at 70iterations 0.1929702 3.416473 at 80iterations 0.1077907 2.040108 at 90iterations 6.0387962E-02 1.200508 at 100iterations 3.4047931E-02 0.6032844 at 110iterations 1.9575847E-02 0.3845978 at 120iterations 1.1630164E-02 0.2344723 at 130iterations 7.2582006E-03 0.1575699 at 140iterations 4.8691649E-03 0.1008224 at 150iterations 3.5140447E-03 7.1594238E-02 at 160iterations 2.6908678E-03 5.2337646E-02 at 170iterations 2.1350824E-03 4.2457581E-02 at 180iterations finished qdiffx linear iterations at : 19:56:33 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 2.1350824E-03 4.2457581E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 19:56:34 13.220u 0.214s 0:13.78 97.4% 0+0k 0+0io 0pf+0w