Sat Oct 8 11:42:37 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 Sat Oct 8 2011 at 11:42:37 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 = 3372 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: 0.5509385 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): -4.293000 52.22400 ymin,ymax (A): 32.21700 95.55500 zmin,zma (A): -23.02900 41.58800 x,y,z range (A): 56.51700 63.33800 64.61700 scale (grids/A): 0.5509385 object centre (A): 23.96550 63.88600 9.279500 number of atom coordinates read : 3372 total number of charged atoms : 3221 net assigned charge : 3.500015 assigned positive charge : 526.7777 centred at (gu) : 90.58578 87.40119 89.76891 assigned negative charge : -523.2787 centred at (gu) : 90.72413 87.36723 89.68724 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6737 nv = 96 ne = 84 npr = 63490 no. pairs analyzed = 63490 no. exposed pairs = 4585 no. arc points = 34269 no. surface atoms = 1533 nbur = 1839 mkacc time = 0.1100000 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 = 1.568000 m= 262 mr = 3070 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3586 ## 539 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1501842E-10 9.7835418E-10 midg,1,midg; midg,igrid,midg -8.2794084E-11 3.1970465E-10 1,midg,midg; igrid,midg,midg 1.3407154E-09 -1.1926408E-09 gauss-seidel spectral radius is 0.9830576 estimated iterations to convergence 63 setup time was (sec) 0.4300000 now iterating at: 11:42:38 rms-change max change #iterations 7.9339661E-02 12.58002 at 10iterations 5.4129297E-03 0.7775669 at 20iterations 3.7023856E-04 5.9005737E-02 at 30iterations 2.5275556E-05 3.5634041E-03 at 40iterations 1.6977671E-06 2.4271011E-04 at 50iterations finished qdiffx linear iterations at : 11:42:41 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.6977671E-06 2.4271011E-04 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 11:42:41 3.577u 0.191s 0:04.15 90.6% 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 Sat Oct 8 2011 at 11:42:41 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 = 3372 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: 1.652816 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): -4.293000 52.22400 ymin,ymax (A): 32.21700 95.55500 zmin,zma (A): -23.02900 41.58800 x,y,z range (A): 56.51700 63.33800 64.61700 scale (grids/A): 1.652816 object centre (A): 23.96550 63.88600 9.279500 number of atom coordinates read : 3372 total number of charged atoms : 3221 net assigned charge : 3.500015 assigned positive charge : 526.7777 centred at (gu) : 91.75625 82.20286 89.30582 assigned negative charge : -523.2787 centred at (gu) : 92.17204 82.10121 89.06120 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34269 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20801 mr = 45832 m= 2244 mr = 13334 m= 60 mr = 1092 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2258 time to turn everything in is 0.3500000 number of dielectric boundary points 36281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 437 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 24697 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) : 0.5509385 object centre at (A) : 23.96550 63.88600 9.279500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7243771E-02 9.6235387E-03 midg,1,midg; midg,igrid,midg 1.3094981E-02 9.5216418E-03 1,midg,midg; igrid,midg,midg 7.2503895E-03 -4.4345106E-03 gauss-seidel spectral radius is 0.9982797 estimated iterations to convergence 191 setup time was (sec) 0.5800000 now iterating at: 11:42:42 rms-change max change #iterations 3.674608 147.0203 at 10iterations 1.558343 55.67018 at 20iterations 0.6614143 22.49644 at 30iterations 0.2820641 10.70448 at 40iterations 0.1197611 4.000103 at 50iterations 5.0875276E-02 1.670260 at 60iterations 2.1625178E-02 0.7474508 at 70iterations 9.2355693E-03 0.3138809 at 80iterations 3.9285412E-03 0.1319838 at 90iterations 1.6746557E-03 5.2831650E-02 at 100iterations 7.1609725E-04 2.4441719E-02 at 110iterations 3.0354664E-04 1.0475159E-02 at 120iterations finished qdiffx linear iterations at : 11:42:50 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 3.0354664E-04 1.0475159E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 11:42:50 8.140u 0.225s 0:08.76 95.4% 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 Sat Oct 8 2011 at 11:42:50 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 = 3372 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: 2.479223 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): -4.293000 52.22400 ymin,ymax (A): 32.21700 95.55500 zmin,zma (A): -23.02900 41.58800 x,y,z range (A): 56.51700 63.33800 64.61700 scale (grids/A): 2.479223 object centre (A): 23.96550 63.88600 9.279500 number of atom coordinates read : 3372 total number of charged atoms : 3221 net assigned charge : 3.500015 assigned positive charge : 526.7777 centred at (gu) : 92.63410 78.30400 88.95846 assigned negative charge : -523.2787 centred at (gu) : 93.25803 78.15178 88.59162 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 170405 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34269 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 72052 mr = 113176 m= 20028 mr = 54621 m= 3480 mr = 14301 m= 308 mr = 2263 m= 5 mr = 160 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 7648 time to turn everything in is 0.8900000 number of dielectric boundary points 81757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 25730 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) : 1.652816 object centre at (A) : 23.96550 63.88600 9.279500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3353107 2.5982482E-02 midg,1,midg; midg,igrid,midg 0.1282217 3.7610170E-02 1,midg,midg; igrid,midg,midg 6.5116569E-02 -7.0684448E-02 gauss-seidel spectral radius is 0.9991833 estimated iterations to convergence 276 setup time was (sec) 1.140000 now iterating at: 11:42:51 rms-change max change #iterations 9.697938 325.4539 at 10iterations 5.542023 137.7675 at 20iterations 3.148163 74.00974 at 30iterations 1.783277 40.09118 at 40iterations 1.006697 21.95651 at 50iterations 0.5674165 12.46971 at 60iterations 0.3181323 5.957370 at 70iterations 0.1788420 3.851052 at 80iterations 0.1000474 2.217712 at 90iterations 5.5992432E-02 1.244017 at 100iterations 3.1350721E-02 0.6111827 at 110iterations 1.7460825E-02 0.3797796 at 120iterations 9.7775524E-03 0.1954384 at 130iterations 5.4529393E-03 0.1052456 at 140iterations 3.0551732E-03 5.6244254E-02 at 150iterations 1.7053762E-03 3.3017159E-02 at 160iterations 9.5050439E-04 1.9456863E-02 at 170iterations 5.3070922E-04 1.0650635E-02 at 180iterations finished qdiffx linear iterations at : 11:43:04 total time elapsed so far: 13.16000 # loops : 180 mean,max change (kT/e) : 5.3070922E-04 1.0650635E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 11:43:04 13.285u 0.235s 0:13.83 97.6% 0+0k 0+0io 0pf+0w