Sat Oct 8 21:48:55 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 21:48:55 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2526 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLM 127 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6592226 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): -5.802000 42.83500 ymin,ymax (A): -21.22200 32.78100 zmin,zma (A): 2.752000 55.13700 x,y,z range (A): 48.63700 54.00300 52.38500 scale (grids/A): 0.6592226 object centre (A): 18.51650 5.779501 28.94450 number of atom coordinates read : 2526 total number of charged atoms : 2384 net assigned charge : 3.920002 assigned positive charge : 380.2979 centred at (gu) : 88.98898 89.25061 91.92628 assigned negative charge : -376.3783 centred at (gu) : 89.00642 89.26041 91.87920 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7504 nv = 96 ne = 84 npr = 50637 no. pairs analyzed = 50637 no. exposed pairs = 3120 no. arc points = 21982 no. surface atoms = 1053 nbur = 1473 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4119 m= 4 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2076 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8698 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5349270E-10 2.7252369E-08 midg,1,midg; midg,igrid,midg 1.3154289E-08 6.5815557E-09 1,midg,midg; igrid,midg,midg 1.5648617E-08 5.0949058E-09 gauss-seidel spectral radius is 0.9880694 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 21:48:56 rms-change max change #iterations 0.1641130 22.62115 at 10iterations 1.7830130E-02 2.511982 at 20iterations 1.8786273E-03 0.2854424 at 30iterations 2.2232710E-04 3.1055450E-02 at 40iterations 3.8519669E-05 4.8835278E-03 at 50iterations finished qdiffx linear iterations at : 21:48:59 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 3.8519669E-05 4.8835278E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 21:49:00 3.568u 0.245s 0:04.08 93.1% 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 Sat Oct 8 2011 at 21:49:00 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2526 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLM 127 has a net charge of -0.0940 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: 1.977668 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): -5.802000 42.83500 ymin,ymax (A): -21.22200 32.78100 zmin,zma (A): 2.752000 55.13700 x,y,z range (A): 48.63700 54.00300 52.38500 scale (grids/A): 1.977668 object centre (A): 18.51650 5.779501 28.94450 number of atom coordinates read : 2526 total number of charged atoms : 2384 net assigned charge : 3.920002 assigned positive charge : 380.2979 centred at (gu) : 86.96617 87.75131 95.77823 assigned negative charge : -376.3783 centred at (gu) : 87.01890 87.78101 95.63715 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 80674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21982 grid for indexing accessible points = 1.400000 m= 30648 mr = 56603 m= 5350 mr = 22338 m= 458 mr = 3320 m= 9 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 34671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18837 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) : 0.6592226 object centre at (A) : 18.51650 5.779501 28.94450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6381484E-02 3.1209217E-02 midg,1,midg; midg,igrid,midg -2.1339998E-02 -2.8205585E-02 1,midg,midg; igrid,midg,midg 3.8362276E-02 1.7703976E-02 gauss-seidel spectral radius is 0.9987275 estimated iterations to convergence 222 setup time was (sec) 0.9100000 now iterating at: 21:49:01 rms-change max change #iterations 4.542360 220.1447 at 10iterations 2.193402 75.02716 at 20iterations 1.052860 35.03925 at 30iterations 0.5078424 16.81482 at 40iterations 0.2449190 8.485107 at 50iterations 0.1178297 3.457630 at 60iterations 5.6562576E-02 1.837341 at 70iterations 2.7236007E-02 0.8236885 at 80iterations 1.3127121E-02 0.4236298 at 90iterations 6.3073905E-03 0.1850471 at 100iterations 3.0543408E-03 8.6845160E-02 at 110iterations 1.4687616E-03 4.3914318E-02 at 120iterations finished qdiffx linear iterations at : 21:49:08 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 1.4687616E-03 4.3914318E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 21:49:08 8.243u 0.261s 0:08.78 96.8% 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 8 2011 at 21:49:08 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2526 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLM 127 has a net charge of -0.0940 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: 2.966502 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): -5.802000 42.83500 ymin,ymax (A): -21.22200 32.78100 zmin,zma (A): 2.752000 55.13700 x,y,z range (A): 48.63700 54.00300 52.38500 scale (grids/A): 2.966502 object centre (A): 18.51650 5.779501 28.94450 number of atom coordinates read : 2526 total number of charged atoms : 2384 net assigned charge : 3.920002 assigned positive charge : 380.2979 centred at (gu) : 85.44923 86.62698 98.66725 assigned negative charge : -376.3783 centred at (gu) : 85.52828 86.67146 98.45571 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 186285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21982 grid for indexing accessible points = 1.400000 m= 97781 mr = 136825 m= 36889 mr = 80103 m= 9881 mr = 29084 m= 1858 mr = 7256 m= 171 mr = 1310 m= 3 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.510000 number of dielectric boundary points 78197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 19072 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) : 1.977668 object centre at (A) : 18.51650 5.779501 28.94450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3401446 0.3093451 midg,1,midg; midg,igrid,midg -0.5457467 -0.5053595 1,midg,midg; igrid,midg,midg 0.4953722 7.4444264E-02 gauss-seidel spectral radius is 0.9992942 estimated iterations to convergence 297 setup time was (sec) 1.860000 now iterating at: 21:49:10 rms-change max change #iterations 10.62498 382.0569 at 10iterations 6.344283 146.8439 at 20iterations 3.771118 81.73728 at 30iterations 2.232911 48.02952 at 40iterations 1.316630 26.86676 at 50iterations 0.7755297 14.00072 at 60iterations 0.4558755 8.767424 at 70iterations 0.2668204 5.037620 at 80iterations 0.1564646 2.785532 at 90iterations 9.1389179E-02 1.693005 at 100iterations 5.3541992E-02 0.9318161 at 110iterations 3.1265084E-02 0.5796709 at 120iterations 1.8221058E-02 0.3078613 at 130iterations 1.0645065E-02 0.1943817 at 140iterations 6.2291329E-03 0.1151004 at 150iterations 3.6322009E-03 7.7239037E-02 at 160iterations 2.1186238E-03 4.0029526E-02 at 170iterations 1.2367881E-03 2.0931244E-02 at 180iterations finished qdiffx linear iterations at : 21:49:22 total time elapsed so far: 13.51000 # loops : 180 mean,max change (kT/e) : 1.2367881E-03 2.0931244E-02 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.68000 DelPhi exited at 21:49:23 13.684u 0.295s 0:14.31 97.6% 0+0k 0+0io 0pf+0w