Sun Oct 9 14:36:40 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 Sun Oct 9 2011 at 14:36:40 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 = 1378 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: 0.9068215 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): -1.695000 37.56300 ymin,ymax (A): -13.85900 21.13800 zmin,zma (A): -13.94300 22.95400 x,y,z range (A): 39.25800 34.99700 36.89700 scale (grids/A): 0.9068215 object centre (A): 17.93400 3.639500 4.505500 number of atom coordinates read : 1378 total number of charged atoms : 1252 net assigned charge : 0.5000027 assigned positive charge : 203.9293 centred at (gu) : 89.81635 90.30878 90.67619 assigned negative charge : -203.4291 centred at (gu) : 89.53226 90.23430 90.87718 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7972 nv = 96 ne = 84 npr = 29755 no. pairs analyzed = 29755 no. exposed pairs = 1657 no. arc points = 12165 no. surface atoms = 558 nbur = 820 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 810 mr = 4663 m= 13 mr = 231 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2200000 number of dielectric boundary points 3901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 623 ## 31 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6676 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0236751E-06 -2.1496176E-06 midg,1,midg; midg,igrid,midg -5.5180931E-07 1.0164827E-06 1,midg,midg; igrid,midg,midg -2.9088658E-06 2.9953421E-06 gauss-seidel spectral radius is 0.9935699 estimated iterations to convergence 101 setup time was (sec) 0.4400000 now iterating at: 14:36:40 rms-change max change #iterations 0.4215623 56.89201 at 10iterations 8.0256052E-02 9.176201 at 20iterations 1.5594107E-02 1.769287 at 30iterations 2.9832299E-03 0.3879471 at 40iterations 5.7134643E-04 6.3442230E-02 at 50iterations finished qdiffx linear iterations at : 14:36:43 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 5.7134643E-04 6.3442230E-02 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 14:36:43 3.037u 0.134s 0:03.45 91.5% 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 Sun Oct 9 2011 at 14:36:43 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 = 1378 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: 2.720465 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): -1.695000 37.56300 ymin,ymax (A): -13.85900 21.13800 zmin,zma (A): -13.94300 22.95400 x,y,z range (A): 39.25800 34.99700 36.89700 scale (grids/A): 2.720465 object centre (A): 17.93400 3.639500 4.505500 number of atom coordinates read : 1378 total number of charged atoms : 1252 net assigned charge : 0.5000027 assigned positive charge : 203.9293 centred at (gu) : 89.44930 90.92663 92.02880 assigned negative charge : -203.4291 centred at (gu) : 88.59677 90.70295 92.63154 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 80924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12165 grid for indexing accessible points = 1.400000 m= 36773 mr = 56666 m= 11106 mr = 29253 m= 2213 mr = 8222 m= 210 mr = 1409 m= 6 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 598 time to turn everything in is 0.6000000 number of dielectric boundary points 35592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 10012 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) : 0.9068215 object centre at (A) : 17.93400 3.639500 4.505500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9824947E-02 1.1248719E-02 midg,1,midg; midg,igrid,midg -6.2950507E-02 -7.8019753E-02 1,midg,midg; igrid,midg,midg 2.7990036E-02 0.1192128 gauss-seidel spectral radius is 0.9991439 estimated iterations to convergence 270 setup time was (sec) 0.8600000 now iterating at: 14:36:44 rms-change max change #iterations 5.491792 219.2674 at 10iterations 3.036709 90.66937 at 20iterations 1.662547 49.93028 at 30iterations 0.9130116 23.91883 at 40iterations 0.5014920 13.19567 at 50iterations 0.2747596 7.642799 at 60iterations 0.1505896 3.761322 at 70iterations 8.2770631E-02 2.254701 at 80iterations 4.5247145E-02 1.246752 at 90iterations 2.4859639E-02 0.7315445 at 100iterations 1.3612509E-02 0.3453989 at 110iterations 7.4784360E-03 0.1908016 at 120iterations finished qdiffx linear iterations at : 14:36:50 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 7.4784360E-03 0.1908016 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 14:36:51 6.958u 0.177s 0:07.40 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 Sun Oct 9 2011 at 14:36:51 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 = 1378 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: 4.080697 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): -1.695000 37.56300 ymin,ymax (A): -13.85900 21.13800 zmin,zma (A): -13.94300 22.95400 x,y,z range (A): 39.25800 34.99700 36.89700 scale (grids/A): 4.080697 object centre (A): 17.93400 3.639500 4.505500 number of atom coordinates read : 1378 total number of charged atoms : 1252 net assigned charge : 0.5000027 assigned positive charge : 203.9293 centred at (gu) : 89.17394 91.38996 93.04314 assigned negative charge : -203.4291 centred at (gu) : 87.89519 91.05443 93.94728 start vw surface at 0.1100000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 185468 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12165 grid for indexing accessible points = 1.400000 m= 106049 mr = 135201 m= 54537 mr = 90308 m= 22640 mr = 46857 m= 7728 mr = 18434 m= 2021 mr = 6054 m= 332 mr = 1459 m= 15 mr = 228 m= 0 mr = 6 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 2116 time to turn everything in is 2.020000 number of dielectric boundary points 80243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 10016 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) : 2.720465 object centre at (A) : 17.93400 3.639500 4.505500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4323029 0.1748808 midg,1,midg; midg,igrid,midg -0.3773946 -0.7001052 1,midg,midg; igrid,midg,midg 0.6840713 0.5201291 gauss-seidel spectral radius is 0.9993463 estimated iterations to convergence 308 setup time was (sec) 2.290000 now iterating at: 14:36:53 rms-change max change #iterations 11.02324 231.8325 at 10iterations 6.525168 132.1754 at 20iterations 3.871284 68.20411 at 30iterations 2.301728 37.36012 at 40iterations 1.364861 22.53605 at 50iterations 0.8097298 12.70254 at 60iterations 0.4804329 7.340486 at 70iterations 0.2862214 4.166757 at 80iterations 0.1693606 2.574181 at 90iterations 0.1005924 1.585779 at 100iterations 5.9876524E-02 0.8990870 at 110iterations 3.5532780E-02 0.5688047 at 120iterations 2.1139488E-02 0.3178952 at 130iterations 1.2559345E-02 0.1905847 at 140iterations 7.4680815E-03 0.1085739 at 150iterations 4.4556800E-03 6.6108704E-02 at 160iterations 2.6607439E-03 4.0348053E-02 at 170iterations 1.5895349E-03 2.3017883E-02 at 180iterations finished qdiffx linear iterations at : 14:37:03 total time elapsed so far: 11.79000 # loops : 180 mean,max change (kT/e) : 1.5895349E-03 2.3017883E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 14:37:03 11.970u 0.187s 0:12.43 97.7% 0+0k 0+0io 0pf+0w