Mon Oct 10 14:13:29 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 Mon Oct 10 2011 at 14:13:29 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2534 !!! WARNING: ADP 668 has a net charge of -2.0000 !!! WARNING: MG6 670 has a net charge of 1.4000 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: 0.5985205 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): -8.984000 50.49600 ymin,ymax (A): -15.99200 34.39800 zmin,zma (A): 79.31800 130.5750 x,y,z range (A): 59.48000 50.39000 51.25701 scale (grids/A): 0.5985205 object centre (A): 20.75600 9.202999 104.9465 number of atom coordinates read : 2534 total number of charged atoms : 2401 net assigned charge : -2.599990 assigned positive charge : 391.5358 centred at (gu) : 92.41477 89.82251 89.39046 assigned negative charge : -394.1365 centred at (gu) : 92.37150 89.93554 89.53635 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6237 nv = 96 ne = 84 npr = 48588 no. pairs analyzed = 48588 no. exposed pairs = 3547 no. arc points = 25124 no. surface atoms = 1186 nbur = 1348 mkacc time = 8.0000006E-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 = 1.456000 m= 319 mr = 3096 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3429 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2527 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7620 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5157678E-09 -5.5206648E-09 midg,1,midg; midg,igrid,midg 2.9102105E-09 -4.9520308E-09 1,midg,midg; igrid,midg,midg -1.5494751E-09 7.2829898E-10 gauss-seidel spectral radius is 0.9855574 estimated iterations to convergence 68 setup time was (sec) 0.3800000 now iterating at: 14:13:30 rms-change max change #iterations 0.1050501 17.33910 at 10iterations 8.9043239E-03 1.828576 at 20iterations 7.5066654E-04 0.1489792 at 30iterations 7.0650887E-05 1.0099888E-02 at 40iterations 9.2710006E-06 1.6193390E-03 at 50iterations finished qdiffx linear iterations at : 14:13:33 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 9.2710006E-06 1.6193390E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 14:13:34 3.366u 0.162s 0:04.19 84.0% 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 14:13:34 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2534 !!! WARNING: ADP 668 has a net charge of -2.0000 !!! WARNING: MG6 670 has a net charge of 1.4000 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: 1.795561 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): -8.984000 50.49600 ymin,ymax (A): -15.99200 34.39800 zmin,zma (A): 79.31800 130.5750 x,y,z range (A): 59.48000 50.39000 51.25701 scale (grids/A): 1.795561 object centre (A): 20.75600 9.202999 104.9465 number of atom coordinates read : 2534 total number of charged atoms : 2401 net assigned charge : -2.599990 assigned positive charge : 391.5358 centred at (gu) : 97.24397 89.46702 88.17078 assigned negative charge : -394.1365 centred at (gu) : 97.11443 89.80652 88.60895 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 67124 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25124 grid for indexing accessible points = 1.400000 m= 22758 mr = 44305 m= 3389 mr = 15642 m= 177 mr = 1917 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 31527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 217 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 18713 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) : 0.5985205 object centre at (A) : 20.75600 9.202999 104.9465 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3613358E-03 -2.9461445E-02 midg,1,midg; midg,igrid,midg 1.9669492E-04 -1.8446058E-02 1,midg,midg; igrid,midg,midg 2.3811888E-02 2.1104250E-02 gauss-seidel spectral radius is 0.9984784 estimated iterations to convergence 203 setup time was (sec) 0.5500000 now iterating at: 14:13:34 rms-change max change #iterations 3.820652 181.1988 at 10iterations 1.701416 65.54315 at 20iterations 0.7614634 29.40269 at 30iterations 0.3407610 12.13906 at 40iterations 0.1526578 5.036972 at 50iterations 6.8456411E-02 2.316258 at 60iterations 3.0662663E-02 1.091949 at 70iterations 1.3727237E-02 0.5155869 at 80iterations 6.1763800E-03 0.2268181 at 90iterations 2.7658362E-03 0.1004763 at 100iterations 1.2422624E-03 4.3479919E-02 at 110iterations 5.5880385E-04 1.9050598E-02 at 120iterations finished qdiffx linear iterations at : 14:13:41 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 5.5880385E-04 1.9050598E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 14:13:42 7.652u 0.192s 0:08.24 95.1% 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 14:13:42 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2534 !!! WARNING: ADP 668 has a net charge of -2.0000 !!! WARNING: MG6 670 has a net charge of 1.4000 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: 2.693342 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): -8.984000 50.49600 ymin,ymax (A): -15.99200 34.39800 zmin,zma (A): 79.31800 130.5750 x,y,z range (A): 59.48000 50.39000 51.25701 scale (grids/A): 2.693342 object centre (A): 20.75600 9.202999 104.9465 number of atom coordinates read : 2534 total number of charged atoms : 2401 net assigned charge : -2.599990 assigned positive charge : 391.5358 centred at (gu) : 100.8657 89.20035 87.25612 assigned negative charge : -394.1365 centred at (gu) : 100.6715 89.70971 87.91330 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 155389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25124 grid for indexing accessible points = 1.400000 m= 74702 mr = 108592 m= 25506 mr = 58429 m= 5879 mr = 19366 m= 813 mr = 4116 m= 42 mr = 561 m= 0 mr = 23 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8300000 number of dielectric boundary points 71244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 19203 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) : 1.795561 object centre at (A) : 20.75600 9.202999 104.9465 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4658938E-02 -0.3422118 midg,1,midg; midg,igrid,midg -4.3589868E-02 -0.1440323 1,midg,midg; igrid,midg,midg 0.3587632 0.1611389 gauss-seidel spectral radius is 0.9992225 estimated iterations to convergence 283 setup time was (sec) 1.060000 now iterating at: 14:13:43 rms-change max change #iterations 9.460107 302.3214 at 10iterations 5.536106 123.5405 at 20iterations 3.198783 82.64078 at 30iterations 1.842685 37.58282 at 40iterations 1.056246 21.90749 at 50iterations 0.6035641 12.96261 at 60iterations 0.3434820 7.293225 at 70iterations 0.1958183 3.690086 at 80iterations 0.1113964 2.472857 at 90iterations 6.3289464E-02 1.235968 at 100iterations 3.5974275E-02 0.8268471 at 110iterations 2.0355461E-02 0.4345636 at 120iterations 1.1543853E-02 0.2309475 at 130iterations 6.5465975E-03 0.1327019 at 140iterations 3.7079421E-03 7.3948860E-02 at 150iterations 2.1021934E-03 4.1511536E-02 at 160iterations 1.1907473E-03 2.4644852E-02 at 170iterations 6.7484553E-04 1.3420105E-02 at 180iterations finished qdiffx linear iterations at : 14:13:54 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 6.7484553E-04 1.3420105E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 14:13:55 12.296u 0.205s 0:12.87 97.0% 0+0k 0+0io 0pf+0w