Tue Oct 11 08:23:12 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+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 Tue Oct 11 2011 at 08:23:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2142 !!! WARNING: ASP 696 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7100119 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): 37.21700 82.10900 ymin,ymax (A): 28.82400 78.20800 zmin,zma (A): 1.328000 51.46800 x,y,z range (A): 44.89200 49.38400 50.14000 scale (grids/A): 0.7100119 object centre (A): 59.66300 53.51600 26.39800 number of atom coordinates read : 2142 total number of charged atoms : 2022 net assigned charge : 1.000009 assigned positive charge : 317.0015 centred at (gu) : 89.37707 89.82981 89.75547 assigned negative charge : -316.0020 centred at (gu) : 89.32672 89.83997 89.52966 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7342 nv = 96 ne = 84 npr = 44355 no. pairs analyzed = 44355 no. exposed pairs = 2739 no. arc points = 19353 no. surface atoms = 919 nbur = 1223 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 453 mr = 3975 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2900000 number of dielectric boundary points 3761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1699 ## 125 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8158 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1850704E-07 1.2071521E-07 midg,1,midg; midg,igrid,midg 1.5501659E-08 4.1110098E-09 1,midg,midg; igrid,midg,midg -1.9560192E-08 3.2037121E-08 gauss-seidel spectral radius is 0.9896724 estimated iterations to convergence 80 setup time was (sec) 0.5200000 now iterating at: 08:23:13 rms-change max change #iterations 0.2046052 30.81937 at 10iterations 2.5342740E-02 3.363535 at 20iterations 3.1285626E-03 0.4386530 at 30iterations 4.1417731E-04 5.4595947E-02 at 40iterations 6.6883600E-05 1.1247635E-02 at 50iterations finished qdiffx linear iterations at : 08:23:15 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 6.6883600E-05 1.1247635E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 08:23:16 3.378u 0.181s 0:04.33 81.9% 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 Tue Oct 11 2011 at 08:23:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2142 !!! WARNING: ASP 696 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.130036 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): 37.21700 82.10900 ymin,ymax (A): 28.82400 78.20800 zmin,zma (A): 1.328000 51.46800 x,y,z range (A): 44.89200 49.38400 50.14000 scale (grids/A): 2.130036 object centre (A): 59.66300 53.51600 26.39800 number of atom coordinates read : 2142 total number of charged atoms : 2022 net assigned charge : 1.000009 assigned positive charge : 317.0015 centred at (gu) : 88.13071 89.48920 89.26597 assigned negative charge : -316.0020 centred at (gu) : 87.98010 89.51986 88.58910 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 78142 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19353 grid for indexing accessible points = 1.400000 m= 29548 mr = 53748 m= 5994 mr = 21824 m= 562 mr = 3805 m= 20 mr = 221 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 203 time to turn everything in is 0.6200000 number of dielectric boundary points 34668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 16066 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) : 0.7100119 object centre at (A) : 59.66300 53.51600 26.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2494282E-02 7.0960090E-02 midg,1,midg; midg,igrid,midg -4.0990707E-02 -3.3777550E-02 1,midg,midg; igrid,midg,midg -1.0088215E-02 5.0006849E-03 gauss-seidel spectral radius is 0.9988554 estimated iterations to convergence 234 setup time was (sec) 0.9200000 now iterating at: 08:23:18 rms-change max change #iterations 4.698703 208.1921 at 10iterations 2.335050 76.87228 at 20iterations 1.169486 35.80678 at 30iterations 0.5833352 18.08680 at 40iterations 0.2919894 8.242756 at 50iterations 0.1460885 4.402494 at 60iterations 7.2603270E-02 2.190805 at 70iterations 3.6302648E-02 0.9982300 at 80iterations 1.8177679E-02 0.5753880 at 90iterations 9.0818787E-03 0.2664394 at 100iterations 4.5298091E-03 0.1453104 at 110iterations 2.2706224E-03 6.6871643E-02 at 120iterations finished qdiffx linear iterations at : 08:23:24 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.2706224E-03 6.6871643E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 08:23:25 8.035u 0.238s 0:08.58 96.2% 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 Tue Oct 11 2011 at 08:23:25 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2142 !!! WARNING: ASP 696 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: 3.195054 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): 37.21700 82.10900 ymin,ymax (A): 28.82400 78.20800 zmin,zma (A): 1.328000 51.46800 x,y,z range (A): 44.89200 49.38400 50.14000 scale (grids/A): 3.195054 object centre (A): 59.66300 53.51600 26.39800 number of atom coordinates read : 2142 total number of charged atoms : 2022 net assigned charge : 1.000009 assigned positive charge : 317.0015 centred at (gu) : 87.19608 89.23382 88.89898 assigned negative charge : -316.0020 centred at (gu) : 86.97027 89.27969 87.88364 start vw surface at 0.1200000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 180745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19353 grid for indexing accessible points = 1.400000 m= 92213 mr = 130636 m= 37851 mr = 75353 m= 11113 mr = 30536 m= 2197 mr = 8267 m= 251 mr = 1492 m= 13 mr = 111 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 657 time to turn everything in is 1.890000 number of dielectric boundary points 77988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 16176 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) : 2.130036 object centre at (A) : 59.66300 53.51600 26.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5744581 0.3477925 midg,1,midg; midg,igrid,midg -0.4386697 -0.3052814 1,midg,midg; igrid,midg,midg -0.1116862 3.9591109E-03 gauss-seidel spectral radius is 0.9993150 estimated iterations to convergence 301 setup time was (sec) 2.190000 now iterating at: 08:23:27 rms-change max change #iterations 10.46141 418.4387 at 10iterations 6.196891 120.9939 at 20iterations 3.677159 78.34628 at 30iterations 2.177079 42.53422 at 40iterations 1.281348 24.68105 at 50iterations 0.7580720 14.61869 at 60iterations 0.4463793 8.152058 at 70iterations 0.2619328 4.501376 at 80iterations 0.1542278 2.644918 at 90iterations 9.0619139E-02 1.604725 at 100iterations 5.3270198E-02 0.8821564 at 110iterations 3.1260379E-02 0.5085278 at 120iterations 1.8372808E-02 0.3757668 at 130iterations 1.0789095E-02 0.1715274 at 140iterations 6.3345041E-03 9.9300385E-02 at 150iterations 3.7192034E-03 6.1744690E-02 at 160iterations 2.1864471E-03 3.6955357E-02 at 170iterations 1.2824158E-03 2.1779060E-02 at 180iterations finished qdiffx linear iterations at : 08:23:38 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 1.2824158E-03 2.1779060E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 08:23:38 12.661u 0.212s 0:13.19 97.5% 0+0k 0+0io 0pf+0w