Sat Oct 15 14:57:27 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 15 2011 at 14:57:27 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: HIR 108 has a net charge of 0.5140 !!! WARNING: HIR 234 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6149806 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): -13.49500 39.27600 ymin,ymax (A): -35.89900 21.98900 zmin,zma (A): 6.689000 63.48300 x,y,z range (A): 52.77100 57.88800 56.79400 scale (grids/A): 0.6149806 object centre (A): 12.89050 -6.955001 35.08600 number of atom coordinates read : 2749 total number of charged atoms : 2610 net assigned charge : 10.52803 assigned positive charge : 409.5245 centred at (gu) : 90.34367 92.55727 88.47649 assigned negative charge : -398.9978 centred at (gu) : 90.42830 92.62797 88.48095 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7029 nv = 96 ne = 84 npr = 54350 no. pairs analyzed = 54350 no. exposed pairs = 3743 no. arc points = 26532 no. surface atoms = 1254 nbur = 1495 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 378 mr = 3573 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2000000 number of dielectric boundary points 3790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2634 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8620 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0554939E-08 5.1121414E-09 midg,1,midg; midg,igrid,midg 6.5823462E-09 5.2992051E-09 1,midg,midg; igrid,midg,midg 1.1331531E-08 2.4956759E-09 gauss-seidel spectral radius is 0.9863313 estimated iterations to convergence 70 setup time was (sec) 0.4500000 now iterating at: 14:57:28 rms-change max change #iterations 0.1234931 17.00024 at 10iterations 1.1056878E-02 1.604403 at 20iterations 1.0238861E-03 0.1640911 at 30iterations 9.7690252E-05 1.6387939E-02 at 40iterations 1.0508639E-05 1.2969971E-03 at 50iterations finished qdiffx linear iterations at : 14:57:31 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 1.0508639E-05 1.2969971E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 14:57:31 4.020u 0.250s 0:04.55 93.8% 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 15 2011 at 14:57:32 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: HIR 108 has a net charge of 0.5140 !!! WARNING: HIR 234 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.844942 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): -13.49500 39.27600 ymin,ymax (A): -35.89900 21.98900 zmin,zma (A): 6.689000 63.48300 x,y,z range (A): 52.77100 57.88800 56.79400 scale (grids/A): 1.844942 object centre (A): 12.89050 -6.955001 35.08600 number of atom coordinates read : 2749 total number of charged atoms : 2610 net assigned charge : 10.52803 assigned positive charge : 409.5245 centred at (gu) : 91.03027 97.67118 85.42884 assigned negative charge : -398.9978 centred at (gu) : 91.28477 97.88363 85.44286 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76859 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26532 grid for indexing accessible points = 1.400000 m= 26441 mr = 51502 m= 3897 mr = 18520 m= 198 mr = 2283 m= 0 mr = 57 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 957 time to turn everything in is 0.4000000 number of dielectric boundary points 35033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20460 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) : 0.6149806 object centre at (A) : 12.89050 -6.955001 35.08600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1144538E-02 1.6213702E-02 midg,1,midg; midg,igrid,midg 2.7179062E-02 4.8362713E-02 1,midg,midg; igrid,midg,midg 2.3659751E-02 3.3853572E-02 gauss-seidel spectral radius is 0.9985706 estimated iterations to convergence 210 setup time was (sec) 0.6700000 now iterating at: 14:57:32 rms-change max change #iterations 4.079302 204.8709 at 10iterations 1.861567 74.49658 at 20iterations 0.8594729 27.93693 at 30iterations 0.3940884 13.08956 at 40iterations 0.1816539 6.408051 at 50iterations 8.3441451E-02 2.857665 at 60iterations 3.8262978E-02 1.270362 at 70iterations 1.7588573E-02 0.5446377 at 80iterations 8.1228828E-03 0.2657909 at 90iterations 3.7299052E-03 0.1132050 at 100iterations 1.7161720E-03 6.2986374E-02 at 110iterations 7.8854058E-04 2.5650024E-02 at 120iterations finished qdiffx linear iterations at : 14:57:41 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 7.8854058E-04 2.5650024E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.340000 DelPhi exited at 14:57:41 9.342u 0.310s 0:09.97 96.7% 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 15 2011 at 14:57:42 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: HIR 108 has a net charge of 0.5140 !!! WARNING: HIR 234 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.767413 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): -13.49500 39.27600 ymin,ymax (A): -35.89900 21.98900 zmin,zma (A): 6.689000 63.48300 x,y,z range (A): 52.77100 57.88800 56.79400 scale (grids/A): 2.767413 object centre (A): 12.89050 -6.955001 35.08600 number of atom coordinates read : 2749 total number of charged atoms : 2610 net assigned charge : 10.52803 assigned positive charge : 409.5245 centred at (gu) : 91.54522 101.5065 83.14317 assigned negative charge : -398.9978 centred at (gu) : 91.92718 101.8254 83.16425 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 177942 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26532 grid for indexing accessible points = 1.400000 m= 86246 mr = 125658 m= 29985 mr = 68383 m= 6709 mr = 23341 m= 788 mr = 4824 m= 48 mr = 469 m= 0 mr = 21 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 3396 time to turn everything in is 1.030000 number of dielectric boundary points 79022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 20878 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) : 1.844942 object centre at (A) : 12.89050 -6.955001 35.08600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2029893 0.2714193 midg,1,midg; midg,igrid,midg 0.2227153 0.8527456 1,midg,midg; igrid,midg,midg 0.1929536 0.5634836 gauss-seidel spectral radius is 0.9992595 estimated iterations to convergence 290 setup time was (sec) 1.330000 now iterating at: 14:57:43 rms-change max change #iterations 9.963574 285.3003 at 10iterations 5.898408 144.5885 at 20iterations 3.457169 84.65849 at 30iterations 2.012791 48.03336 at 40iterations 1.169756 22.46788 at 50iterations 0.6779956 12.83088 at 60iterations 0.3915185 8.461941 at 70iterations 0.2261089 4.242296 at 80iterations 0.1304598 2.402905 at 90iterations 7.5084493E-02 1.424520 at 100iterations 4.3215014E-02 0.7507868 at 110iterations 2.4855953E-02 0.4846039 at 120iterations 1.4306946E-02 0.2540131 at 130iterations 8.2241530E-03 0.1516418 at 140iterations 4.7269636E-03 9.2407227E-02 at 150iterations 2.7188682E-03 5.0907135E-02 at 160iterations 1.5602108E-03 3.1892776E-02 at 170iterations 8.9597632E-04 1.6601563E-02 at 180iterations finished qdiffx linear iterations at : 14:57:57 total time elapsed so far: 15.28000 # loops : 180 mean,max change (kT/e) : 8.9597632E-04 1.6601563E-02 energy calculations done at 15.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.40000 DelPhi exited at 14:57:58 15.405u 0.332s 0:16.03 98.1% 0+0k 0+0io 0pf+0w