Sat Oct 8 11:34:24 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 11:34:24 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4399 !!! WARNING: HIR 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5761357 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): -25.74200 36.04900 ymin,ymax (A): 37.30500 95.23400 zmin,zma (A): 30.75500 87.85400 x,y,z range (A): 61.79100 57.92900 57.09901 scale (grids/A): 0.5761357 object centre (A): 5.153501 66.26950 59.30450 number of atom coordinates read : 4399 total number of charged atoms : 4246 net assigned charge : 1.4038846E-02 assigned positive charge : 662.4365 centred at (gu) : 90.51071 88.69814 88.95583 assigned negative charge : -662.4252 centred at (gu) : 90.36090 88.86923 89.10806 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9272 nv = 96 ne = 84 npr = 93306 no. pairs analyzed = 93306 no. exposed pairs = 4872 no. arc points = 33066 no. surface atoms = 1655 nbur = 2744 mkacc time = 0.1600000 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 = 1.512000 m= 401 mr = 5428 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.3100000 number of dielectric boundary points 4213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3539 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 12328 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3628311E-09 -3.5827261E-09 midg,1,midg; midg,igrid,midg 6.4242647E-09 -3.7842858E-09 1,midg,midg; igrid,midg,midg -4.0034056E-09 4.6371578E-09 gauss-seidel spectral radius is 0.9845500 estimated iterations to convergence 66 setup time was (sec) 0.5000000 now iterating at: 11:34:25 rms-change max change #iterations 0.1182142 15.56332 at 10iterations 9.4129508E-03 1.325256 at 20iterations 8.8941853E-04 0.1032104 at 30iterations 1.6621240E-04 2.2138596E-02 at 40iterations 5.2828789E-05 7.2525740E-03 at 50iterations finished qdiffx linear iterations at : 11:34:28 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 5.2828789E-05 7.2525740E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 11:34:28 3.587u 0.184s 0:04.22 89.0% 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 Sat Oct 8 2011 at 11:34:28 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4399 !!! WARNING: HIR 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.728407 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): -25.74200 36.04900 ymin,ymax (A): 37.30500 95.23400 zmin,zma (A): 30.75500 87.85400 x,y,z range (A): 61.79100 57.92900 57.09901 scale (grids/A): 1.728407 object centre (A): 5.153501 66.26950 59.30450 number of atom coordinates read : 4399 total number of charged atoms : 4246 net assigned charge : 1.4038846E-02 assigned positive charge : 662.4365 centred at (gu) : 91.53064 86.09325 86.86602 assigned negative charge : -662.4252 centred at (gu) : 91.08237 86.60748 87.32369 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 103671 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33066 grid for indexing accessible points = 1.400000 m= 34959 mr = 75661 m= 4407 mr = 25865 m= 142 mr = 2630 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 6832 time to turn everything in is 0.4900000 number of dielectric boundary points 39007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 32887 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) : 0.5761357 object centre at (A) : 5.153501 66.26950 59.30450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8158622E-02 -3.2082666E-02 midg,1,midg; midg,igrid,midg 3.8111035E-02 -1.6850593E-02 1,midg,midg; igrid,midg,midg -1.4847322E-02 4.2407773E-02 gauss-seidel spectral radius is 0.9985057 estimated iterations to convergence 205 setup time was (sec) 0.7200000 now iterating at: 11:34:29 rms-change max change #iterations 4.740069 193.0524 at 10iterations 2.144741 61.09391 at 20iterations 0.9692451 28.19125 at 30iterations 0.4395247 12.93642 at 40iterations 0.1988910 5.141619 at 50iterations 9.0552688E-02 2.584401 at 60iterations 4.0940240E-02 1.093839 at 70iterations 1.8603126E-02 0.5158645 at 80iterations 8.4820995E-03 0.2517738 at 90iterations 3.8640026E-03 0.1045151 at 100iterations 1.7741753E-03 4.9188614E-02 at 110iterations 8.2554464E-04 2.3976326E-02 at 120iterations finished qdiffx linear iterations at : 11:34:37 total time elapsed so far: 8.110000 # loops : 120 mean,max change (kT/e) : 8.2554464E-04 2.3976326E-02 energy calculations done at 8.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 11:34:38 8.244u 0.213s 0:09.21 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 11:34:38 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4399 !!! WARNING: HIR 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.592611 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): -25.74200 36.04900 ymin,ymax (A): 37.30500 95.23400 zmin,zma (A): 30.75500 87.85400 x,y,z range (A): 61.79100 57.92900 57.09901 scale (grids/A): 2.592611 object centre (A): 5.153501 66.26950 59.30450 number of atom coordinates read : 4399 total number of charged atoms : 4246 net assigned charge : 1.4038846E-02 assigned positive charge : 662.4365 centred at (gu) : 92.29579 84.13967 85.29877 assigned negative charge : -662.4252 centred at (gu) : 91.62338 84.91116 85.98540 start vw surface at 0.1100000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 241083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33066 grid for indexing accessible points = 1.400000 m= 119077 mr = 183831 m= 37385 mr = 98378 m= 7490 mr = 29748 m= 765 mr = 5527 m= 16 mr = 426 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 22858 time to turn everything in is 1.250000 number of dielectric boundary points 87906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 33955 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) : 1.728407 object centre at (A) : 5.153501 66.26950 59.30450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6408570 -0.4292103 midg,1,midg; midg,igrid,midg 0.4472491 -0.2383350 1,midg,midg; igrid,midg,midg -0.2300491 0.4604882 gauss-seidel spectral radius is 0.9992501 estimated iterations to convergence 288 setup time was (sec) 1.500000 now iterating at: 11:34:39 rms-change max change #iterations 11.64448 302.5848 at 10iterations 6.805959 130.6413 at 20iterations 3.952764 75.04627 at 30iterations 2.291795 43.21647 at 40iterations 1.320423 22.95681 at 50iterations 0.7632539 13.98275 at 60iterations 0.4396808 7.040050 at 70iterations 0.2526444 4.308743 at 80iterations 0.1453612 2.367853 at 90iterations 8.3334684E-02 1.366884 at 100iterations 4.7893375E-02 0.8437694 at 110iterations 2.7500317E-02 0.4679031 at 120iterations 1.5771283E-02 0.2655201 at 130iterations 9.0902550E-03 0.1480289 at 140iterations 5.2233492E-03 8.4131241E-02 at 150iterations 3.0232307E-03 4.8202515E-02 at 160iterations 1.7581667E-03 2.9332161E-02 at 170iterations 1.0401517E-03 1.6556263E-02 at 180iterations finished qdiffx linear iterations at : 11:34:51 total time elapsed so far: 13.59000 # loops : 180 mean,max change (kT/e) : 1.0401517E-03 1.6556263E-02 energy calculations done at 13.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.72000 DelPhi exited at 11:34:52 13.720u 0.224s 0:14.65 95.1% 0+0k 0+0io 0pf+0w