Thu Dec 22 10:40:23 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 Thu Dec 22 2011 at 10:40:25 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2475 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: 0.5726050 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): -11.81200 37.17300 ymin,ymax (A): -28.34400 22.17900 zmin,zma (A): 31.73700 93.90900 x,y,z range (A): 48.98500 50.52300 62.17200 scale (grids/A): 0.5726050 object centre (A): 12.68050 -3.082500 62.82300 number of atom coordinates read : 2475 total number of charged atoms : 2339 net assigned charge : -7.999981 assigned positive charge : 329.3683 centred at (gu) : 91.45456 88.19672 91.07822 assigned negative charge : -337.3690 centred at (gu) : 91.38847 88.24052 91.34323 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5575 nv = 96 ne = 84 npr = 51501 no. pairs analyzed = 51501 no. exposed pairs = 3566 no. arc points = 25166 no. surface atoms = 1196 nbur = 1279 mkacc time = 9.9999994E-02 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 = 1.512000 m= 273 mr = 2566 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3278 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2294 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 6793 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5353750E-09 -6.2853758E-09 midg,1,midg; midg,igrid,midg -1.1231100E-09 -1.2441002E-09 1,midg,midg; igrid,midg,midg -1.5533101E-09 -6.3383898E-10 gauss-seidel spectral radius is 0.9842377 estimated iterations to convergence 65 setup time was (sec) 0.4300000 now iterating at: 10:40:26 rms-change max change #iterations 7.5787731E-02 14.36438 at 10iterations 6.1052446E-03 1.124777 at 20iterations 7.6956267E-04 0.1225357 at 30iterations 1.8449711E-04 2.8908253E-02 at 40iterations 5.2435022E-05 8.4781647E-03 at 50iterations finished qdiffx linear iterations at : 10:40:29 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 5.2435022E-05 8.4781647E-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) 3.550000 DelPhi exited at 10:40:37 3.556u 0.191s 0:15.52 24.0% 0+0k 0+45832io 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 Thu Dec 22 2011 at 10:40:41 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2475 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: 1.717815 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): -11.81200 37.17300 ymin,ymax (A): -28.34400 22.17900 zmin,zma (A): 31.73700 93.90900 x,y,z range (A): 48.98500 50.52300 62.17200 scale (grids/A): 1.717815 object centre (A): 12.68050 -3.082500 62.82300 number of atom coordinates read : 2475 total number of charged atoms : 2339 net assigned charge : -7.999981 assigned positive charge : 329.3683 centred at (gu) : 94.36314 84.59005 93.23455 assigned negative charge : -337.3690 centred at (gu) : 94.16523 84.72153 94.02958 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 60624 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25166 grid for indexing accessible points = 1.400000 m= 18946 mr = 38466 m= 2372 mr = 12099 m= 84 mr = 1115 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 30335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 18181 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) : 0.5726050 object centre at (A) : 12.68050 -3.082500 62.82300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3323476E-02 -4.8077967E-02 midg,1,midg; midg,igrid,midg -6.4056332E-04 -3.1722451E-03 1,midg,midg; igrid,midg,midg -6.7584626E-03 -3.3238924E-03 gauss-seidel spectral radius is 0.9983407 estimated iterations to convergence 195 setup time was (sec) 0.5900000 now iterating at: 10:40:42 rms-change max change #iterations 3.176877 163.3829 at 10iterations 1.367238 63.09176 at 20iterations 0.5873552 22.76036 at 30iterations 0.2553633 10.01456 at 40iterations 0.1106817 3.832066 at 50iterations 4.7916993E-02 1.814312 at 60iterations 2.0829616E-02 0.7785025 at 70iterations 9.0483865E-03 0.3558350 at 80iterations 3.9702514E-03 0.1487770 at 90iterations 1.7478584E-03 6.6810608E-02 at 100iterations 7.8268308E-04 2.9464722E-02 at 110iterations 3.6296691E-04 1.4549255E-02 at 120iterations finished qdiffx linear iterations at : 10:40:49 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 3.6296691E-04 1.4549255E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 10:40:58 8.035u 0.242s 0:17.29 47.8% 0+0k 0+45224io 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 Thu Dec 22 2011 at 10:40:59 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2475 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: 2.576722 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): -11.81200 37.17300 ymin,ymax (A): -28.34400 22.17900 zmin,zma (A): 31.73700 93.90900 x,y,z range (A): 48.98500 50.52300 62.17200 scale (grids/A): 2.576722 object centre (A): 12.68050 -3.082500 62.82300 number of atom coordinates read : 2475 total number of charged atoms : 2339 net assigned charge : -7.999981 assigned positive charge : 329.3683 centred at (gu) : 96.54456 81.88500 94.85174 assigned negative charge : -337.3690 centred at (gu) : 96.24786 82.08226 96.04452 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 140333 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25166 grid for indexing accessible points = 1.400000 m= 63155 mr = 94840 m= 19709 mr = 47593 m= 3755 mr = 13954 m= 345 mr = 2343 m= 9 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9700000 number of dielectric boundary points 68434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 18705 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) : 1.717815 object centre at (A) : 12.68050 -3.082500 62.82300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3153940 -0.5920442 midg,1,midg; midg,igrid,midg -5.3460654E-03 -2.4537917E-02 1,midg,midg; igrid,midg,midg -5.9093945E-02 -3.1984705E-02 gauss-seidel spectral radius is 0.9991888 estimated iterations to convergence 277 setup time was (sec) 1.190000 now iterating at: 10:41:04 rms-change max change #iterations 8.077334 295.9625 at 10iterations 4.657875 146.0813 at 20iterations 2.669971 70.75729 at 30iterations 1.523099 37.57613 at 40iterations 0.8630896 20.65940 at 50iterations 0.4885533 11.39481 at 60iterations 0.2758329 6.731550 at 70iterations 0.1556752 4.130386 at 80iterations 8.7304518E-02 1.920946 at 90iterations 4.9143177E-02 1.004154 at 100iterations 2.7585851E-02 0.6024950 at 110iterations 1.5496845E-02 0.3162155 at 120iterations 8.7088030E-03 0.1786461 at 130iterations 4.8931073E-03 0.1238744 at 140iterations 2.7579605E-03 6.2545776E-02 at 150iterations 1.5652946E-03 3.5162926E-02 at 160iterations 8.9273107E-04 2.1656990E-02 at 170iterations 5.1941053E-04 1.1028290E-02 at 180iterations finished qdiffx linear iterations at : 10:41:15 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 5.1941053E-04 1.1028290E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 10:42:09 12.806u 0.232s 1:10.01 18.6% 0+0k 0+45216io 0pf+0w