Mon Oct 10 14:03:31 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 Mon Oct 10 2011 at 14:03:32 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6633623 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): -12.68500 40.98100 ymin,ymax (A): -25.81700 21.96700 zmin,zma (A): -7.487000 36.14000 x,y,z range (A): 53.66600 47.78400 43.62700 scale (grids/A): 0.6633623 object centre (A): 14.14800 -1.925000 14.32650 number of atom coordinates read : 2148 total number of charged atoms : 2006 net assigned charge : -9.371978 assigned positive charge : 323.5198 centred at (gu) : 88.46325 91.12619 89.02287 assigned negative charge : -332.8919 centred at (gu) : 88.75127 91.18510 89.14622 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6423 nv = 96 ne = 84 npr = 44282 no. pairs analyzed = 44282 no. exposed pairs = 2638 no. arc points = 18971 no. surface atoms = 891 nbur = 1257 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3570 m= 8 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.1800000 number of dielectric boundary points 3172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1824 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7387 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1156532E-09 -4.0881304E-08 midg,1,midg; midg,igrid,midg -1.2979194E-08 -4.7607404E-08 1,midg,midg; igrid,midg,midg 3.4764813E-08 -5.9455207E-08 gauss-seidel spectral radius is 0.9881824 estimated iterations to convergence 75 setup time was (sec) 0.3600000 now iterating at: 14:03:32 rms-change max change #iterations 0.1625288 25.04686 at 10iterations 1.7267536E-02 3.040218 at 20iterations 1.8537052E-03 0.2675591 at 30iterations 2.0028141E-04 3.2539368E-02 at 40iterations 2.1570804E-05 3.3051968E-03 at 50iterations finished qdiffx linear iterations at : 14:03:35 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 2.1570804E-05 3.3051968E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:03:37 3.338u 0.186s 0:04.76 73.7% 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 Mon Oct 10 2011 at 14:03:37 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.990087 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): -12.68500 40.98100 ymin,ymax (A): -25.81700 21.96700 zmin,zma (A): -7.487000 36.14000 x,y,z range (A): 53.66600 47.78400 43.62700 scale (grids/A): 1.990087 object centre (A): 14.14800 -1.925000 14.32650 number of atom coordinates read : 2148 total number of charged atoms : 2006 net assigned charge : -9.371978 assigned positive charge : 323.5198 centred at (gu) : 85.38943 93.37830 87.06837 assigned negative charge : -332.8919 centred at (gu) : 86.25362 93.55513 87.43871 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18971 grid for indexing accessible points = 1.400000 m= 26872 mr = 47048 m= 4985 mr = 20608 m= 346 mr = 3385 m= 4 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3389 time to turn everything in is 0.3500000 number of dielectric boundary points 29252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 15859 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) : 0.6633623 object centre at (A) : 14.14800 -1.925000 14.32650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1522653E-03 -3.1867497E-02 midg,1,midg; midg,igrid,midg -3.5382539E-03 -1.5720552E-02 1,midg,midg; igrid,midg,midg 3.4885235E-02 -8.8705905E-02 gauss-seidel spectral radius is 0.9986985 estimated iterations to convergence 220 setup time was (sec) 0.5600000 now iterating at: 14:03:37 rms-change max change #iterations 4.215313 197.0725 at 10iterations 2.008672 82.62970 at 20iterations 0.9544027 37.68488 at 30iterations 0.4541925 16.54419 at 40iterations 0.2172011 7.505082 at 50iterations 0.1033704 3.271902 at 60iterations 4.9064487E-02 1.735596 at 70iterations 2.3444375E-02 0.7770691 at 80iterations 1.1178094E-02 0.3607302 at 90iterations 5.3216764E-03 0.1803169 at 100iterations 2.5307673E-03 8.8517189E-02 at 110iterations 1.2094214E-03 4.1381836E-02 at 120iterations finished qdiffx linear iterations at : 14:03:44 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 1.2094214E-03 4.1381836E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 14:03:45 7.698u 0.187s 0:08.52 92.3% 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 Mon Oct 10 2011 at 14:03:45 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.985130 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): -12.68500 40.98100 ymin,ymax (A): -25.81700 21.96700 zmin,zma (A): -7.487000 36.14000 x,y,z range (A): 53.66600 47.78400 43.62700 scale (grids/A): 2.985130 object centre (A): 14.14800 -1.925000 14.32650 number of atom coordinates read : 2148 total number of charged atoms : 2006 net assigned charge : -9.371978 assigned positive charge : 323.5198 centred at (gu) : 83.08403 95.06738 85.60248 assigned negative charge : -332.8919 centred at (gu) : 84.38044 95.33279 86.15800 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 157172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18971 grid for indexing accessible points = 1.400000 m= 83656 mr = 113410 m= 34151 mr = 69639 m= 9330 mr = 28505 m= 1495 mr = 7345 m= 104 mr = 1044 m= 0 mr = 65 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 11906 time to turn everything in is 0.8900000 number of dielectric boundary points 65900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 16048 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) : 1.990087 object centre at (A) : 14.14800 -1.925000 14.32650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0002983E-02 -0.2906511 midg,1,midg; midg,igrid,midg -2.2227859E-02 -5.3602528E-02 1,midg,midg; igrid,midg,midg 0.4736737 -0.8392825 gauss-seidel spectral radius is 0.9992648 estimated iterations to convergence 291 setup time was (sec) 1.110000 now iterating at: 14:03:46 rms-change max change #iterations 9.663556 355.7009 at 10iterations 5.594564 130.7528 at 20iterations 3.236305 60.73913 at 30iterations 1.869728 41.15770 at 40iterations 1.077101 20.44194 at 50iterations 0.6211784 14.57095 at 60iterations 0.3574614 6.738293 at 70iterations 0.2057642 4.035944 at 80iterations 0.1184271 2.120504 at 90iterations 6.8102114E-02 1.379013 at 100iterations 3.9146230E-02 0.7286377 at 110iterations 2.2554379E-02 0.4401321 at 120iterations 1.2981312E-02 0.2844810 at 130iterations 7.4401060E-03 0.1347747 at 140iterations 4.2888471E-03 8.5628510E-02 at 150iterations 2.4675042E-03 4.9108356E-02 at 160iterations 1.4186739E-03 2.5966644E-02 at 170iterations 8.1744976E-04 1.6330719E-02 at 180iterations finished qdiffx linear iterations at : 14:03:57 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 8.1744976E-04 1.6330719E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 14:03:58 12.285u 0.211s 0:13.02 95.9% 0+0k 0+0io 0pf+0w