Tue Oct 11 08:18:08 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 Tue Oct 11 2011 at 08:18:08 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2767 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6354533 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): -5.050000 50.97300 ymin,ymax (A): -16.25000 29.52500 zmin,zma (A): 57.27500 109.4010 x,y,z range (A): 56.02300 45.77500 52.12600 scale (grids/A): 0.6354533 object centre (A): 22.96150 6.637500 83.33800 number of atom coordinates read : 2767 total number of charged atoms : 2615 net assigned charge : 5.312018 assigned positive charge : 419.3376 centred at (gu) : 90.01147 90.22101 89.43632 assigned negative charge : -414.0262 centred at (gu) : 90.25776 90.13937 89.47737 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7513 nv = 96 ne = 84 npr = 55976 no. pairs analyzed = 55976 no. exposed pairs = 3255 no. arc points = 23057 no. surface atoms = 1102 nbur = 1665 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 4282 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 109 time to turn everything in is 0.2100000 number of dielectric boundary points 3556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2287 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9004 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2705818E-08 2.0236046E-09 midg,1,midg; midg,igrid,midg -2.1505413E-09 1.6427608E-08 1,midg,midg; igrid,midg,midg 3.3037217E-08 -2.1087299E-08 gauss-seidel spectral radius is 0.9871838 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 08:18:08 rms-change max change #iterations 0.1487167 22.77195 at 10iterations 1.4929901E-02 2.062370 at 20iterations 1.9993614E-03 0.3436203 at 30iterations 4.8312065E-04 0.1027145 at 40iterations 1.4288154E-04 3.2032013E-02 at 50iterations finished qdiffx linear iterations at : 08:18:11 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.4288154E-04 3.2032013E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:18:12 3.355u 0.155s 0:03.79 92.3% 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 Tue Oct 11 2011 at 08:18:12 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2767 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.906360 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): -5.050000 50.97300 ymin,ymax (A): -16.25000 29.52500 zmin,zma (A): 57.27500 109.4010 x,y,z range (A): 56.02300 45.77500 52.12600 scale (grids/A): 1.906360 object centre (A): 22.96150 6.637500 83.33800 number of atom coordinates read : 2767 total number of charged atoms : 2615 net assigned charge : 5.312018 assigned positive charge : 419.3376 centred at (gu) : 90.03390 90.66236 88.30838 assigned negative charge : -414.0262 centred at (gu) : 90.77296 90.41779 88.43181 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23057 grid for indexing accessible points = 1.400000 m= 29490 mr = 57342 m= 4613 mr = 22235 m= 257 mr = 3060 m= 4 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 5406 time to turn everything in is 0.3900000 number of dielectric boundary points 32760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20563 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) : 0.6354533 object centre at (A) : 22.96150 6.637500 83.33800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2109626E-03 6.9096256E-03 midg,1,midg; midg,igrid,midg 1.2092014E-02 1.9899426E-02 1,midg,midg; igrid,midg,midg 4.7810782E-02 -3.6150280E-02 gauss-seidel spectral radius is 0.9986507 estimated iterations to convergence 216 setup time was (sec) 0.6100000 now iterating at: 08:18:12 rms-change max change #iterations 4.427516 176.7133 at 10iterations 2.080825 66.45509 at 20iterations 0.9763351 29.43983 at 30iterations 0.4594192 14.24656 at 40iterations 0.2166799 6.583580 at 50iterations 0.1018446 3.112011 at 60iterations 4.7959246E-02 1.464577 at 70iterations 2.2811117E-02 0.7699509 at 80iterations 1.0805742E-02 0.3788033 at 90iterations 5.1692817E-03 0.1709671 at 100iterations 2.5304502E-03 8.2248688E-02 at 110iterations 1.2922214E-03 4.5757294E-02 at 120iterations finished qdiffx linear iterations at : 08:18:19 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.2922214E-03 4.5757294E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 08:18:20 7.677u 0.207s 0:08.21 95.8% 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 Tue Oct 11 2011 at 08:18:20 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2767 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.859540 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): -5.050000 50.97300 ymin,ymax (A): -16.25000 29.52500 zmin,zma (A): 57.27500 109.4010 x,y,z range (A): 56.02300 45.77500 52.12600 scale (grids/A): 2.859540 object centre (A): 22.96150 6.637500 83.33800 number of atom coordinates read : 2767 total number of charged atoms : 2615 net assigned charge : 5.312018 assigned positive charge : 419.3376 centred at (gu) : 90.05064 90.99346 87.46248 assigned negative charge : -414.0262 centred at (gu) : 91.15931 90.62669 87.64757 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 187949 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23057 grid for indexing accessible points = 1.400000 m= 95729 mr = 138822 m= 34598 mr = 79523 m= 8249 mr = 28355 m= 1166 mr = 6477 m= 49 mr = 792 m= 0 mr = 19 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 17357 time to turn everything in is 1.030000 number of dielectric boundary points 73752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 20918 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) : 1.906360 object centre at (A) : 22.96150 6.637500 83.33800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1443459E-02 1.4859022E-02 midg,1,midg; midg,igrid,midg 0.1966199 0.2123088 1,midg,midg; igrid,midg,midg 0.5737159 -0.2437821 gauss-seidel spectral radius is 0.9992589 estimated iterations to convergence 290 setup time was (sec) 1.250000 now iterating at: 08:18:21 rms-change max change #iterations 10.26168 356.0681 at 10iterations 5.954077 119.1867 at 20iterations 3.441859 63.66283 at 30iterations 1.982208 35.90430 at 40iterations 1.139198 19.29025 at 50iterations 0.6565928 11.42653 at 60iterations 0.3772688 6.616436 at 70iterations 0.2174568 4.151919 at 80iterations 0.1249262 2.176716 at 90iterations 7.1699768E-02 1.304535 at 100iterations 4.1252360E-02 0.7491302 at 110iterations 2.3694048E-02 0.4307308 at 120iterations 1.3655636E-02 0.2350788 at 130iterations 7.8851534E-03 0.1344124 at 140iterations 4.5535364E-03 8.0081940E-02 at 150iterations 2.6586789E-03 5.0842285E-02 at 160iterations 1.5725230E-03 3.3733368E-02 at 170iterations 9.5395598E-04 2.1026611E-02 at 180iterations finished qdiffx linear iterations at : 08:18:32 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 9.5395598E-04 2.1026611E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 08:18:33 12.436u 0.211s 0:13.02 97.0% 0+0k 0+0io 0pf+0w