Sun Nov 13 17:19:11 PST 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 Nov 13 2011 at 17:19:11 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 ! Automatically converted by prot2crg.py # of charge parameter records: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2563 !!! WARNING: GLU 264 has a net charge of -2.0000 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: 0.6387942 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): 13.14800 58.82100 ymin,ymax (A): 3.810000 53.51900 zmin,zma (A): -25.97200 29.75800 x,y,z range (A): 45.67300 49.70900 55.73000 scale (grids/A): 0.6387942 object centre (A): 35.98450 28.66450 1.893000 number of atom coordinates read : 2563 total number of charged atoms : 2424 net assigned charge : -0.9999928 assigned positive charge : 378.5778 centred at (gu) : 91.46416 90.84857 89.25293 assigned negative charge : -379.5787 centred at (gu) : 91.43708 90.87026 89.41182 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6912 nv = 96 ne = 84 npr = 52191 no. pairs analyzed = 52191 no. exposed pairs = 3518 no. arc points = 24248 no. surface atoms = 1163 nbur = 1400 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 3555 m= 5 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2317 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8360 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8424833E-08 -1.6456131E-08 midg,1,midg; midg,igrid,midg 6.7201961E-10 -4.7455040E-09 1,midg,midg; igrid,midg,midg -3.3286887E-09 1.9838127E-09 gauss-seidel spectral radius is 0.9873050 estimated iterations to convergence 73 setup time was (sec) 0.4500000 now iterating at: 17:19:12 rms-change max change #iterations 0.1383789 21.08135 at 10iterations 1.3592936E-02 1.886312 at 20iterations 1.3634764E-03 0.1922531 at 30iterations 1.4889479E-04 2.0677567E-02 at 40iterations 2.7301612E-05 3.8108826E-03 at 50iterations finished qdiffx linear iterations at : 17:19:15 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 2.7301612E-05 3.8108826E-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) 3.540000 DelPhi exited at 17:19:15 3.541u 0.177s 0:04.00 92.7% 0+0k 0+45824io 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 Nov 13 2011 at 17:19:15 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 ! Automatically converted by prot2crg.py # of charge parameter records: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2563 !!! WARNING: GLU 264 has a net charge of -2.0000 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: 1.916383 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): 13.14800 58.82100 ymin,ymax (A): 3.810000 53.51900 zmin,zma (A): -25.97200 29.75800 x,y,z range (A): 45.67300 49.70900 55.73000 scale (grids/A): 1.916383 object centre (A): 35.98450 28.66450 1.893000 number of atom coordinates read : 2563 total number of charged atoms : 2424 net assigned charge : -0.9999928 assigned positive charge : 378.5778 centred at (gu) : 94.39182 92.54504 87.75817 assigned negative charge : -379.5787 centred at (gu) : 94.31106 92.61058 88.23548 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24248 grid for indexing accessible points = 1.400000 m= 26882 mr = 49794 m= 4622 mr = 19197 m= 269 mr = 2762 m= 2 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 392 time to turn everything in is 0.4600000 number of dielectric boundary points 34529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 19093 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) : 0.6387942 object centre at (A) : 35.98450 28.66450 1.893000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4868264E-02 -4.6140337E-03 midg,1,midg; midg,igrid,midg 5.2680005E-03 -1.4310667E-03 1,midg,midg; igrid,midg,midg -1.0138221E-02 -7.8856573E-03 gauss-seidel spectral radius is 0.9986548 estimated iterations to convergence 216 setup time was (sec) 0.6800000 now iterating at: 17:19:16 rms-change max change #iterations 4.251126 187.4925 at 10iterations 1.997275 81.56864 at 20iterations 0.9439255 33.34675 at 30iterations 0.4448584 14.29376 at 40iterations 0.2096183 6.962099 at 50iterations 9.9184677E-02 3.124664 at 60iterations 4.6579033E-02 1.570926 at 70iterations 2.1900555E-02 0.6935883 at 80iterations 1.0387002E-02 0.3231735 at 90iterations 4.9114651E-03 0.1743631 at 100iterations 2.3412902E-03 7.5363636E-02 at 110iterations 1.1179382E-03 3.5526276E-02 at 120iterations finished qdiffx linear iterations at : 17:19:23 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 1.1179382E-03 3.5526276E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 17:19:24 8.107u 0.222s 0:08.62 96.5% 0+0k 0+45240io 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 Nov 13 2011 at 17:19:24 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 ! Automatically converted by prot2crg.py # of charge parameter records: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2563 !!! WARNING: GLU 264 has a net charge of -2.0000 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: 2.874574 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): 13.14800 58.82100 ymin,ymax (A): 3.810000 53.51900 zmin,zma (A): -25.97200 29.75800 x,y,z range (A): 45.67300 49.70900 55.73000 scale (grids/A): 2.874574 object centre (A): 35.98450 28.66450 1.893000 number of atom coordinates read : 2563 total number of charged atoms : 2424 net assigned charge : -0.9999928 assigned positive charge : 378.5778 centred at (gu) : 96.58772 93.81744 86.63711 assigned negative charge : -379.5787 centred at (gu) : 96.46664 93.91587 87.35313 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 172181 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24248 grid for indexing accessible points = 1.400000 m= 85588 mr = 121389 m= 32490 mr = 68177 m= 8344 mr = 25644 m= 1231 mr = 6122 m= 54 mr = 760 m= 0 mr = 10 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 1385 time to turn everything in is 1.250000 number of dielectric boundary points 77786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19391 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) : 1.916383 object centre at (A) : 35.98450 28.66450 1.893000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9924368 2.4001172E-02 midg,1,midg; midg,igrid,midg 0.1394771 3.6900260E-02 1,midg,midg; igrid,midg,midg -0.2017360 -7.0818856E-02 gauss-seidel spectral radius is 0.9992658 estimated iterations to convergence 291 setup time was (sec) 1.480000 now iterating at: 17:19:26 rms-change max change #iterations 9.950539 378.2292 at 10iterations 5.823431 131.5938 at 20iterations 3.386350 71.76787 at 30iterations 1.965948 43.47026 at 40iterations 1.142023 21.43405 at 50iterations 0.6624253 12.60980 at 60iterations 0.3830021 6.855050 at 70iterations 0.2209731 4.425994 at 80iterations 0.1277749 2.309094 at 90iterations 7.3718622E-02 1.303535 at 100iterations 4.2426679E-02 0.7647171 at 110iterations 2.4463860E-02 0.4674450 at 120iterations 1.4112316E-02 0.2646604 at 130iterations 8.1182411E-03 0.1458435 at 140iterations 4.6860538E-03 8.1957102E-02 at 150iterations 2.6981344E-03 4.8736095E-02 at 160iterations 1.5552139E-03 2.9169083E-02 at 170iterations 8.9814118E-04 1.5950203E-02 at 180iterations finished qdiffx linear iterations at : 17:19:37 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 8.9814118E-04 1.5950203E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 17:19:38 13.153u 0.226s 0:13.68 97.7% 0+0k 0+45232io 0pf+0w