Sat Oct 8 16:31:45 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 16:31:45 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4403 !!! WARNING: GLM 204 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5437855 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): 15.53700 79.11200 ymin,ymax (A): 119.5320 184.9990 zmin,zma (A): -1.115000 59.89200 x,y,z range (A): 63.57500 65.46699 61.00700 scale (grids/A): 0.5437855 object centre (A): 47.32450 152.2655 29.38850 number of atom coordinates read : 4403 total number of charged atoms : 4229 net assigned charge : 5.406039 assigned positive charge : 674.3000 centred at (gu) : 92.03770 89.89621 87.63448 assigned negative charge : -668.8970 centred at (gu) : 92.02557 89.85495 87.66620 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8412 nv = 96 ne = 84 npr = 87775 no. pairs analyzed = 87775 no. exposed pairs = 5511 no. arc points = 38541 no. surface atoms = 1840 nbur = 2563 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 371 mr = 4435 m= 0 mr = 21 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.4300000 number of dielectric boundary points 4327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3934 ## 519 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 11175 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0524912E-09 7.8080892E-12 midg,1,midg; midg,igrid,midg -8.4501808E-11 6.5154232E-10 1,midg,midg; igrid,midg,midg 1.1542739E-10 6.7035238E-10 gauss-seidel spectral radius is 0.9826730 estimated iterations to convergence 63 setup time was (sec) 0.6400000 now iterating at: 16:31:46 rms-change max change #iterations 8.7585188E-02 13.71123 at 10iterations 6.2034032E-03 1.085768 at 20iterations 8.8252546E-04 0.1285782 at 30iterations 2.7814950E-04 3.6533356E-02 at 40iterations 9.7387674E-05 1.2240171E-02 at 50iterations finished qdiffx linear iterations at : 16:31:48 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 9.7387674E-05 1.2240171E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 16:31:49 3.246u 0.139s 0:03.67 91.8% 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 16:31:49 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4403 !!! WARNING: GLM 204 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.631357 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): 15.53700 79.11200 ymin,ymax (A): 119.5320 184.9990 zmin,zma (A): -1.115000 59.89200 x,y,z range (A): 63.57500 65.46699 61.00700 scale (grids/A): 1.631357 object centre (A): 47.32450 152.2655 29.38850 number of atom coordinates read : 4403 total number of charged atoms : 4229 net assigned charge : 5.406039 assigned positive charge : 674.3000 centred at (gu) : 96.11208 89.68724 82.90224 assigned negative charge : -668.8970 centred at (gu) : 96.07610 89.56438 82.99844 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 94053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38541 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30079 mr = 65112 m= 3462 mr = 20422 m= 97 mr = 1765 m= 0 mr = 5 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 644 time to turn everything in is 0.6200000 number of dielectric boundary points 40387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 462 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 32354 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) : 0.5437855 object centre at (A) : 47.32450 152.2655 29.38850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0976589E-03 8.2627526E-03 midg,1,midg; midg,igrid,midg 2.2860322E-02 3.1147089E-02 1,midg,midg; igrid,midg,midg -9.4656115E-03 -1.3626728E-02 gauss-seidel spectral radius is 0.9983261 estimated iterations to convergence 194 setup time was (sec) 0.8900000 now iterating at: 16:31:50 rms-change max change #iterations 4.185031 142.9665 at 10iterations 1.797409 64.78204 at 20iterations 0.7749341 25.98691 at 30iterations 0.3359098 10.41085 at 40iterations 0.1450484 5.033739 at 50iterations 6.2600113E-02 1.841393 at 60iterations 2.7150284E-02 0.8172226 at 70iterations 1.1799637E-02 0.3697281 at 80iterations 5.1599862E-03 0.1607666 at 90iterations 2.3210903E-03 6.9145203E-02 at 100iterations 1.0789598E-03 3.3079147E-02 at 110iterations 5.3689210E-04 1.6704559E-02 at 120iterations finished qdiffx linear iterations at : 16:31:56 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 5.3689210E-04 1.6704559E-02 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 16:31:56 7.231u 0.185s 0:07.78 95.2% 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 16:31:56 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4403 !!! WARNING: GLM 204 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.447035 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): 15.53700 79.11200 ymin,ymax (A): 119.5320 184.9990 zmin,zma (A): -1.115000 59.89200 x,y,z range (A): 63.57500 65.46699 61.00700 scale (grids/A): 2.447035 object centre (A): 47.32450 152.2655 29.38850 number of atom coordinates read : 4403 total number of charged atoms : 4229 net assigned charge : 5.406039 assigned positive charge : 674.3000 centred at (gu) : 99.16794 89.53059 79.35311 assigned negative charge : -668.8970 centred at (gu) : 99.11407 89.34670 79.49750 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 218787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38541 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 103086 mr = 159441 m= 30565 mr = 81124 m= 5458 mr = 22638 m= 410 mr = 3698 m= 3 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 2073 time to turn everything in is 1.570000 number of dielectric boundary points 91220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 33801 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) : 1.631357 object centre at (A) : 47.32450 152.2655 29.38850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4283133E-02 0.1680422 midg,1,midg; midg,igrid,midg 0.3723360 0.5999216 1,midg,midg; igrid,midg,midg -0.1326625 -0.2454112 gauss-seidel spectral radius is 0.9992135 estimated iterations to convergence 282 setup time was (sec) 1.870000 now iterating at: 16:31:58 rms-change max change #iterations 10.89485 408.6794 at 10iterations 6.345788 146.1178 at 20iterations 3.664068 80.06576 at 30iterations 2.106542 44.69367 at 40iterations 1.207094 23.28075 at 50iterations 0.6890647 12.82531 at 60iterations 0.3918778 7.304502 at 70iterations 0.2230121 4.030491 at 80iterations 0.1265122 2.230315 at 90iterations 7.1818158E-02 1.371773 at 100iterations 4.0658638E-02 0.7399139 at 110iterations 2.3071675E-02 0.3983860 at 120iterations 1.3081839E-02 0.2350254 at 130iterations 7.4057514E-03 0.1289659 at 140iterations 4.2253933E-03 7.5544357E-02 at 150iterations 2.4008038E-03 4.3560982E-02 at 160iterations 1.3819314E-03 2.8984070E-02 at 170iterations 8.0576871E-04 1.5563965E-02 at 180iterations finished qdiffx linear iterations at : 16:32:08 total time elapsed so far: 11.84000 # loops : 180 mean,max change (kT/e) : 8.0576871E-04 1.5563965E-02 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 16:32:09 12.031u 0.171s 0:12.50 97.6% 0+0k 0+0io 0pf+0w