Sun Oct 9 23:20:29 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 23:20:29 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 = 2285 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: 0.6663173 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): -11.94300 32.94000 ymin,ymax (A): -22.15300 29.95700 zmin,zma (A): -10.82400 42.60400 x,y,z range (A): 44.88300 52.11000 53.42800 scale (grids/A): 0.6663173 object centre (A): 10.49850 3.901999 15.89000 number of atom coordinates read : 2285 total number of charged atoms : 2145 net assigned charge : 0.5000095 assigned positive charge : 337.8094 centred at (gu) : 91.65665 90.65661 90.58748 assigned negative charge : -337.3098 centred at (gu) : 91.59512 90.58421 90.28320 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6989 nv = 96 ne = 84 npr = 44947 no. pairs analyzed = 44947 no. exposed pairs = 3063 no. arc points = 21359 no. surface atoms = 1023 nbur = 1262 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3733 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2800000 number of dielectric boundary points 3619 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2010 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8041 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5129703E-08 6.8138206E-08 midg,1,midg; midg,igrid,midg -1.2024967E-08 1.7604922E-08 1,midg,midg; igrid,midg,midg -8.1864533E-09 1.8704917E-08 gauss-seidel spectral radius is 0.9883035 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 23:20:30 rms-change max change #iterations 0.1578283 21.88324 at 10iterations 1.7153222E-02 2.574257 at 20iterations 1.8574371E-03 0.2809181 at 30iterations 2.4235241E-04 3.4278870E-02 at 40iterations 6.6097331E-05 1.2231827E-02 at 50iterations finished qdiffx linear iterations at : 23:20:35 total time elapsed so far: 5.100000 # loops : 50 mean,max change (kT/e) : 6.6097331E-05 1.2231827E-02 energy calculations done at 5.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.270000 DelPhi exited at 23:20:35 5.277u 0.462s 0:06.01 95.3% 0+0k 0+0io 6pf+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 23:20:35 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 = 2285 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: 1.998952 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): -11.94300 32.94000 ymin,ymax (A): -22.15300 29.95700 zmin,zma (A): -10.82400 42.60400 x,y,z range (A): 44.88300 52.11000 53.42800 scale (grids/A): 1.998952 object centre (A): 10.49850 3.901999 15.89000 number of atom coordinates read : 2285 total number of charged atoms : 2145 net assigned charge : 0.5000095 assigned positive charge : 337.8094 centred at (gu) : 94.96980 91.96949 91.76225 assigned negative charge : -337.3098 centred at (gu) : 94.78525 91.75254 90.84973 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21359 grid for indexing accessible points = 1.400000 m= 26656 mr = 51099 m= 4339 mr = 19268 m= 328 mr = 2748 m= 5 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 164 time to turn everything in is 0.6600000 number of dielectric boundary points 33273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 16962 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) : 0.6663173 object centre at (A) : 10.49850 3.901999 15.89000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1350453E-02 8.1578288E-03 midg,1,midg; midg,igrid,midg 2.5287019E-02 2.5660187E-02 1,midg,midg; igrid,midg,midg -1.6062602E-02 3.3170281E-03 gauss-seidel spectral radius is 0.9987334 estimated iterations to convergence 223 setup time was (sec) 1.010000 now iterating at: 23:20:37 rms-change max change #iterations 4.303570 214.5579 at 10iterations 2.070095 73.54552 at 20iterations 0.9948957 33.15913 at 30iterations 0.4796382 18.30103 at 40iterations 0.2306231 7.258115 at 50iterations 0.1113440 3.378778 at 60iterations 5.3755634E-02 1.818409 at 70iterations 2.5911251E-02 0.8953490 at 80iterations 1.2509665E-02 0.3871975 at 90iterations 6.0175527E-03 0.1890831 at 100iterations 2.9107670E-03 9.4215393E-02 at 110iterations 1.4106143E-03 4.7373056E-02 at 120iterations finished qdiffx linear iterations at : 23:20:48 total time elapsed so far: 12.53000 # loops : 120 mean,max change (kT/e) : 1.4106143E-03 4.7373056E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 23:20:49 12.714u 0.504s 0:13.48 97.9% 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 Sun Oct 9 2011 at 23:20:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2285 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: 2.998428 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): -11.94300 32.94000 ymin,ymax (A): -22.15300 29.95700 zmin,zma (A): -10.82400 42.60400 x,y,z range (A): 44.88300 52.11000 53.42800 scale (grids/A): 2.998428 object centre (A): 10.49850 3.901999 15.89000 number of atom coordinates read : 2285 total number of charged atoms : 2145 net assigned charge : 0.5000095 assigned positive charge : 337.8094 centred at (gu) : 97.45453 92.95416 92.64332 assigned negative charge : -337.3098 centred at (gu) : 97.17779 92.62881 91.27454 start vw surface at 0.1100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 173344 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21359 grid for indexing accessible points = 1.400000 m= 86222 mr = 123439 m= 30849 mr = 69680 m= 7947 mr = 24595 m= 1427 mr = 5998 m= 129 mr = 1058 m= 0 mr = 90 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 514 time to turn everything in is 1.920000 number of dielectric boundary points 75058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 17159 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) : 1.998952 object centre at (A) : 10.49850 3.901999 15.89000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7451082 -6.9969572E-02 midg,1,midg; midg,igrid,midg 0.2818543 5.1626604E-02 1,midg,midg; igrid,midg,midg -0.2338508 6.7998096E-02 gauss-seidel spectral radius is 0.9992882 estimated iterations to convergence 296 setup time was (sec) 2.310000 now iterating at: 23:20:51 rms-change max change #iterations 10.00671 327.3980 at 10iterations 5.922104 136.2104 at 20iterations 3.495577 86.14410 at 30iterations 2.051951 42.86226 at 40iterations 1.200712 28.86023 at 50iterations 0.7051663 15.21895 at 60iterations 0.4116949 7.860585 at 70iterations 0.2401457 4.836141 at 80iterations 0.1400304 2.806580 at 90iterations 8.1408218E-02 1.419216 at 100iterations 4.7479689E-02 1.008907 at 110iterations 2.7681101E-02 0.5410290 at 120iterations 1.6079931E-02 0.2992001 at 130iterations 9.3730781E-03 0.1741571 at 140iterations 5.4319911E-03 9.4862096E-02 at 150iterations 3.1552000E-03 5.2548409E-02 at 160iterations 1.8371581E-03 3.2066345E-02 at 170iterations 1.0683604E-03 1.8661499E-02 at 180iterations finished qdiffx linear iterations at : 23:21:11 total time elapsed so far: 21.58000 # loops : 180 mean,max change (kT/e) : 1.0683604E-03 1.8661499E-02 energy calculations done at 21.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.75000 DelPhi exited at 23:21:11 21.759u 0.555s 0:22.56 98.8% 0+0k 0+0io 0pf+0w