Mon Oct 10 14:08:33 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 Mon Oct 10 2011 at 14:08:33 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 = 2853 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: 0.6107917 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): 6.917000 60.99400 ymin,ymax (A): -19.44700 38.83800 zmin,zma (A): 38.53300 87.68600 x,y,z range (A): 54.07700 58.28500 49.15301 scale (grids/A): 0.6107917 object centre (A): 33.95550 9.695500 63.10950 number of atom coordinates read : 2853 total number of charged atoms : 2702 net assigned charge : -2.999974 assigned positive charge : 436.6613 centred at (gu) : 89.23769 89.45231 90.80594 assigned negative charge : -439.6621 centred at (gu) : 89.39902 89.59343 90.57234 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7056 nv = 96 ne = 84 npr = 57186 no. pairs analyzed = 57186 no. exposed pairs = 3469 no. arc points = 24227 no. surface atoms = 1172 nbur = 1681 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3945 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2398 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8694 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3177306E-08 1.3276035E-08 midg,1,midg; midg,igrid,midg 6.7437820E-09 -9.0737817E-09 1,midg,midg; igrid,midg,midg 8.4227665E-09 -9.6575441E-09 gauss-seidel spectral radius is 0.9861410 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 14:08:34 rms-change max change #iterations 0.1279392 21.26512 at 10iterations 1.1276718E-02 1.589649 at 20iterations 1.0145104E-03 0.1642466 at 30iterations 8.9695779E-05 1.2420654E-02 at 40iterations 9.0714084E-06 1.3904572E-03 at 50iterations finished qdiffx linear iterations at : 14:08:36 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 9.0714084E-06 1.3904572E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 14:08:37 3.213u 0.173s 0:03.80 88.9% 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 Mon Oct 10 2011 at 14:08:37 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 = 2853 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.832375 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): 6.917000 60.99400 ymin,ymax (A): -19.44700 38.83800 zmin,zma (A): 38.53300 87.68600 x,y,z range (A): 54.07700 58.28500 49.15301 scale (grids/A): 1.832375 object centre (A): 33.95550 9.695500 63.10950 number of atom coordinates read : 2853 total number of charged atoms : 2702 net assigned charge : -2.999974 assigned positive charge : 436.6613 centred at (gu) : 87.71259 88.35616 92.41706 assigned negative charge : -439.6621 centred at (gu) : 88.19662 88.77982 91.71666 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 76792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24227 grid for indexing accessible points = 1.400000 m= 27167 mr = 53984 m= 3962 mr = 20089 m= 177 mr = 2389 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 257 time to turn everything in is 0.6000000 number of dielectric boundary points 31595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 21142 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) : 0.6107917 object centre at (A) : 33.95550 9.695500 63.10950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1996086E-02 1.8957976E-02 midg,1,midg; midg,igrid,midg 0.1044005 -3.2912008E-03 1,midg,midg; igrid,midg,midg -7.1955519E-04 -2.8533030E-02 gauss-seidel spectral radius is 0.9985515 estimated iterations to convergence 208 setup time was (sec) 0.8800000 now iterating at: 14:08:38 rms-change max change #iterations 4.196600 174.5917 at 10iterations 1.919729 71.20615 at 20iterations 0.8788955 36.74190 at 30iterations 0.4052247 12.79381 at 40iterations 0.1856186 6.166168 at 50iterations 8.5208714E-02 2.707503 at 60iterations 3.9011057E-02 1.185110 at 70iterations 1.7951703E-02 0.5358887 at 80iterations 8.2577439E-03 0.2550182 at 90iterations 3.7973791E-03 0.1168537 at 100iterations 1.7624215E-03 5.7861328E-02 at 110iterations 8.2522118E-04 3.1227589E-02 at 120iterations finished qdiffx linear iterations at : 14:08:44 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 8.2522118E-04 3.1227589E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 14:08:45 7.153u 0.213s 0:08.26 89.1% 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 Mon Oct 10 2011 at 14:08:45 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 = 2853 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.748563 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): 6.917000 60.99400 ymin,ymax (A): -19.44700 38.83800 zmin,zma (A): 38.53300 87.68600 x,y,z range (A): 54.07700 58.28500 49.15301 scale (grids/A): 2.748563 object centre (A): 33.95550 9.695500 63.10950 number of atom coordinates read : 2853 total number of charged atoms : 2702 net assigned charge : -2.999974 assigned positive charge : 436.6613 centred at (gu) : 86.56871 87.53414 93.62550 assigned negative charge : -439.6621 centred at (gu) : 87.29479 88.16969 92.57484 start vw surface at 0.2200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 177855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24227 grid for indexing accessible points = 1.400000 m= 89221 mr = 131024 m= 30903 mr = 73159 m= 6968 mr = 24809 m= 836 mr = 5147 m= 26 mr = 506 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 839 time to turn everything in is 1.410000 number of dielectric boundary points 71156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 21614 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) : 1.832375 object centre at (A) : 33.95550 9.695500 63.10950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7045248 0.1500701 midg,1,midg; midg,igrid,midg 1.229876 -0.2237941 1,midg,midg; igrid,midg,midg -4.2851530E-02 -0.2308414 gauss-seidel spectral radius is 0.9992425 estimated iterations to convergence 287 setup time was (sec) 1.690000 now iterating at: 14:08:47 rms-change max change #iterations 10.03583 302.8665 at 10iterations 5.848043 132.2480 at 20iterations 3.383049 68.79208 at 30iterations 1.958524 45.21200 at 40iterations 1.125233 25.64851 at 50iterations 0.6467498 12.92728 at 60iterations 0.3704472 9.255777 at 70iterations 0.2121235 3.784921 at 80iterations 0.1218111 2.147057 at 90iterations 6.9623455E-02 1.268623 at 100iterations 3.9808158E-02 0.7577553 at 110iterations 2.2804044E-02 0.4209366 at 120iterations 1.3037869E-02 0.2329178 at 130iterations 7.4391817E-03 0.1396666 at 140iterations 4.2629661E-03 7.5412750E-02 at 150iterations 2.4372968E-03 4.2175293E-02 at 160iterations 1.3967264E-03 2.3864746E-02 at 170iterations 8.0283906E-04 1.6157150E-02 at 180iterations finished qdiffx linear iterations at : 14:08:57 total time elapsed so far: 11.17000 # loops : 180 mean,max change (kT/e) : 8.0283906E-04 1.6157150E-02 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 14:08:57 11.357u 0.201s 0:12.01 96.1% 0+0k 0+0io 0pf+0w