Sun Oct 9 20:07:33 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 Sun Oct 9 2011 at 20:07:33 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5070 !!! 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5461714 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): 3.265000 68.44600 ymin,ymax (A): -9.083000 53.50400 zmin,zma (A): -0.9860000 62.03300 x,y,z range (A): 65.18100 62.58700 63.01900 scale (grids/A): 0.5461714 object centre (A): 35.85550 22.21050 30.52350 number of atom coordinates read : 5070 total number of charged atoms : 4911 net assigned charge : 1.740050 assigned positive charge : 773.2422 centred at (gu) : 87.71904 89.32005 89.38988 assigned negative charge : -771.5078 centred at (gu) : 87.61806 89.34749 89.35643 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 10049 nv = 96 ne = 84 npr = 102044 no. pairs analyzed = 102044 no. exposed pairs = 5911 no. arc points = 40593 no. surface atoms = 2027 nbur = 3043 mkacc time = 0.2200000 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 = 1.568000 m= 416 mr = 5763 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4101 ## 464 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 13090 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9040081E-10 4.4913578E-10 midg,1,midg; midg,igrid,midg 5.3794691E-10 -1.4964828E-10 1,midg,midg; igrid,midg,midg -1.8670729E-09 7.3275991E-10 gauss-seidel spectral radius is 0.9828712 estimated iterations to convergence 63 setup time was (sec) 0.6900000 now iterating at: 20:07:34 rms-change max change #iterations 0.1040956 12.12733 at 10iterations 1.1841470E-02 1.612427 at 20iterations 4.5144679E-03 0.6912918 at 30iterations 2.1346021E-03 0.3341293 at 40iterations 1.0190330E-03 0.1607704 at 50iterations finished qdiffx linear iterations at : 20:07:36 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 1.0190330E-03 0.1607704 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 20:07:36 3.267u 0.137s 0:03.68 92.1% 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 20:07:36 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5070 !!! 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.638514 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): 3.265000 68.44600 ymin,ymax (A): -9.083000 53.50400 zmin,zma (A): -0.9860000 62.03300 x,y,z range (A): 65.18100 62.58700 63.01900 scale (grids/A): 1.638514 object centre (A): 35.85550 22.21050 30.52350 number of atom coordinates read : 5070 total number of charged atoms : 4911 net assigned charge : 1.740050 assigned positive charge : 773.2422 centred at (gu) : 83.15576 87.95889 88.16808 assigned negative charge : -771.5078 centred at (gu) : 82.85432 88.04222 88.06937 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 112447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40593 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38603 mr = 81710 m= 4510 mr = 28053 m= 137 mr = 2399 m= 0 mr = 14 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 43521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 392 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 37645 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) : 0.5461714 object centre at (A) : 35.85550 22.21050 30.52350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5969569E-02 -1.4846160E-02 midg,1,midg; midg,igrid,midg 2.0061851E-02 1.0508875E-02 1,midg,midg; igrid,midg,midg -1.7387314E-02 1.7231887E-02 gauss-seidel spectral radius is 0.9983947 estimated iterations to convergence 198 setup time was (sec) 1.010000 now iterating at: 20:07:38 rms-change max change #iterations 4.679582 184.7686 at 10iterations 2.051973 58.95747 at 20iterations 0.9062430 27.16978 at 30iterations 0.3990721 10.51890 at 40iterations 0.1763624 5.268721 at 50iterations 7.9048507E-02 2.213858 at 60iterations 3.6268074E-02 0.9790230 at 70iterations 1.7800601E-02 0.5709095 at 80iterations 9.8987333E-03 0.3232117 at 90iterations 6.3145319E-03 0.1996536 at 100iterations 4.4237366E-03 0.1478958 at 110iterations 3.2713632E-03 0.1013718 at 120iterations finished qdiffx linear iterations at : 20:07:44 total time elapsed so far: 7.130000 # loops : 120 mean,max change (kT/e) : 3.2713632E-03 0.1013718 energy calculations done at 7.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.320000 DelPhi exited at 20:07:44 7.320u 0.151s 0:07.75 96.3% 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 20:07:44 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5070 !!! 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.457772 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): 3.265000 68.44600 ymin,ymax (A): -9.083000 53.50400 zmin,zma (A): -0.9860000 62.03300 x,y,z range (A): 65.18100 62.58700 63.01900 scale (grids/A): 2.457772 object centre (A): 35.85550 22.21050 30.52350 number of atom coordinates read : 5070 total number of charged atoms : 4911 net assigned charge : 1.740050 assigned positive charge : 773.2422 centred at (gu) : 79.73343 86.93787 87.25191 assigned negative charge : -771.5078 centred at (gu) : 79.28143 87.06335 87.10412 start vw surface at 0.2100000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 261639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40593 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 131791 mr = 199116 m= 40734 mr = 107878 m= 7322 mr = 31563 m= 582 mr = 4984 m= 14 mr = 298 m= 0 mr = 2 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 98241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 39232 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) : 1.638514 object centre at (A) : 35.85550 22.21050 30.52350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3474522 -0.3527351 midg,1,midg; midg,igrid,midg 0.1947836 2.8768161E-02 1,midg,midg; igrid,midg,midg -0.4233781 0.2638305 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 2.090000 now iterating at: 20:07:46 rms-change max change #iterations 11.86273 357.5616 at 10iterations 6.947483 136.3049 at 20iterations 4.040895 83.65886 at 30iterations 2.344841 48.81105 at 40iterations 1.353992 23.39615 at 50iterations 0.7813004 12.28908 at 60iterations 0.4504358 7.697064 at 70iterations 0.2588471 4.251125 at 80iterations 0.1490209 2.457682 at 90iterations 8.5962914E-02 1.347168 at 100iterations 4.9730189E-02 0.9343872 at 110iterations 2.9151594E-02 0.5297394 at 120iterations 1.7550493E-02 0.3403397 at 130iterations 1.1031873E-02 0.2138252 at 140iterations 7.3525119E-03 0.1503983 at 150iterations 5.2708318E-03 0.1083908 at 160iterations 4.0315832E-03 8.2714081E-02 at 170iterations 3.2248888E-03 6.4506531E-02 at 180iterations finished qdiffx linear iterations at : 20:07:56 total time elapsed so far: 11.83000 # loops : 180 mean,max change (kT/e) : 3.2248888E-03 6.4506531E-02 energy calculations done at 11.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.00000 DelPhi exited at 20:07:57 12.004u 0.173s 0:12.46 97.6% 0+0k 0+0io 0pf+0w