Sat Oct 8 14:40:29 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 14:40:29 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: 367 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3321 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 1 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6373646 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): -12.13800 43.71700 ymin,ymax (A): -22.22300 22.29900 zmin,zma (A): -8.286000 47.20600 x,y,z range (A): 55.85500 44.52200 55.49200 scale (grids/A): 0.6373646 object centre (A): 15.78950 3.7999153E-02 19.46000 number of atom coordinates read : 3321 total number of charged atoms : 2884 net assigned charge : -0.9859930 assigned positive charge : 455.4756 centred at (gu) : 88.80150 89.65020 92.09258 assigned negative charge : -456.4623 centred at (gu) : 88.75718 89.54310 92.03127 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8307 nv = 96 ne = 84 npr = 63040 no. pairs analyzed = 63040 no. exposed pairs = 3495 no. arc points = 24190 no. surface atoms = 1197 nbur = 2124 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 463 mr = 4916 m= 2 mr = 59 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 0.2200000 number of dielectric boundary points 3797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2263 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9966 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8665472E-09 1.0171863E-08 midg,1,midg; midg,igrid,midg -1.6309384E-08 1.1168888E-08 1,midg,midg; igrid,midg,midg -9.1119396E-09 3.2450294E-09 gauss-seidel spectral radius is 0.9872805 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 14:40:30 rms-change max change #iterations 0.1600484 22.11220 at 10iterations 1.5779957E-02 2.172359 at 20iterations 1.7126697E-03 0.3275986 at 30iterations 2.3766099E-04 2.9911041E-02 at 40iterations 4.4950200E-05 6.8626404E-03 at 50iterations finished qdiffx linear iterations at : 14:40:33 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 4.4950200E-05 6.8626404E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:40:33 3.387u 0.189s 0:03.86 92.2% 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 14:40:33 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: 367 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3321 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 1 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: 1.912094 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): -12.13800 43.71700 ymin,ymax (A): -22.22300 22.29900 zmin,zma (A): -8.286000 47.20600 x,y,z range (A): 55.85500 44.52200 55.49200 scale (grids/A): 1.912094 object centre (A): 15.78950 3.7999153E-02 19.46000 number of atom coordinates read : 3321 total number of charged atoms : 2884 net assigned charge : -0.9859930 assigned positive charge : 455.4756 centred at (gu) : 86.40398 88.94993 96.27710 assigned negative charge : -456.4623 centred at (gu) : 86.27123 88.62901 96.09343 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 90385 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24190 grid for indexing accessible points = 1.400000 m= 34035 mr = 65412 m= 5495 mr = 25940 m= 330 mr = 3503 m= 0 mr = 123 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 35267 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 22596 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) : 0.6373646 object centre at (A) : 15.78950 3.7999153E-02 19.46000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5021121E-02 1.7256891E-02 midg,1,midg; midg,igrid,midg -5.6390311E-03 1.8813565E-02 1,midg,midg; igrid,midg,midg -4.5291428E-02 8.0964286E-03 gauss-seidel spectral radius is 0.9986812 estimated iterations to convergence 218 setup time was (sec) 0.6700000 now iterating at: 14:40:34 rms-change max change #iterations 4.709622 183.5789 at 10iterations 2.243288 67.26340 at 20iterations 1.063123 32.26582 at 30iterations 0.5063223 14.93853 at 40iterations 0.2394729 6.381981 at 50iterations 0.1142837 3.987333 at 60iterations 5.4413978E-02 1.599330 at 70iterations 2.5908690E-02 0.7506371 at 80iterations 1.2347440E-02 0.3816290 at 90iterations 5.8912705E-03 0.1639071 at 100iterations 2.8281605E-03 9.5878601E-02 at 110iterations 1.3578943E-03 3.8684845E-02 at 120iterations finished qdiffx linear iterations at : 14:40:41 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.3578943E-03 3.8684845E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 14:40:42 7.867u 0.185s 0:08.38 95.9% 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 14:40:42 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: 367 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3321 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 1 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.868140 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): -12.13800 43.71700 ymin,ymax (A): -22.22300 22.29900 zmin,zma (A): -8.286000 47.20600 x,y,z range (A): 55.85500 44.52200 55.49200 scale (grids/A): 2.868140 object centre (A): 15.78950 3.7999153E-02 19.46000 number of atom coordinates read : 3321 total number of charged atoms : 2884 net assigned charge : -0.9859930 assigned positive charge : 455.4756 centred at (gu) : 84.60582 88.42485 99.41539 assigned negative charge : -456.4623 centred at (gu) : 84.40675 87.94331 99.14019 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 209213 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24190 grid for indexing accessible points = 1.400000 m= 110145 mr = 158084 m= 40938 mr = 92345 m= 10099 mr = 33432 m= 1516 mr = 7677 m= 86 mr = 1010 m= 0 mr = 24 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.140000 number of dielectric boundary points 79425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 23051 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) : 1.912094 object centre at (A) : 15.78950 3.7999153E-02 19.46000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1445146 0.2544484 midg,1,midg; midg,igrid,midg -1.6175235E-02 0.2121741 1,midg,midg; igrid,midg,midg -0.7369768 0.1949438 gauss-seidel spectral radius is 0.9992769 estimated iterations to convergence 293 setup time was (sec) 1.380000 now iterating at: 14:40:43 rms-change max change #iterations 10.95213 336.1645 at 10iterations 6.424374 160.4180 at 20iterations 3.757170 83.48598 at 30iterations 2.192674 46.14806 at 40iterations 1.277234 23.26864 at 50iterations 0.7423277 14.07961 at 60iterations 0.4313793 7.559222 at 70iterations 0.2501229 4.655443 at 80iterations 0.1449670 2.600079 at 90iterations 8.3981924E-02 1.414632 at 100iterations 4.8711907E-02 0.8188248 at 110iterations 2.8158106E-02 0.4223785 at 120iterations 1.6348068E-02 0.2771759 at 130iterations 9.4653619E-03 0.1655750 at 140iterations 5.4913359E-03 8.9664459E-02 at 150iterations 3.2041650E-03 5.5269241E-02 at 160iterations 1.8709872E-03 3.1795382E-02 at 170iterations 1.1015371E-03 1.9833744E-02 at 180iterations finished qdiffx linear iterations at : 14:40:55 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 1.1015371E-03 1.9833744E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 14:40:55 13.012u 0.207s 0:13.53 97.6% 0+0k 0+0io 0pf+0w