Mon Oct 10 09:44:52 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 09:44:52 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 = 2670 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: 0.5817184 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): -17.50900 34.31500 ymin,ymax (A): -61.68100 -2.594000 zmin,zma (A): -0.4859999 60.71200 x,y,z range (A): 51.82400 59.08700 61.19800 scale (grids/A): 0.5817184 object centre (A): 8.402999 -32.13750 30.11300 number of atom coordinates read : 2670 total number of charged atoms : 2525 net assigned charge : 7.000017 assigned positive charge : 389.4982 centred at (gu) : 88.05970 88.69981 88.01086 assigned negative charge : -382.4985 centred at (gu) : 88.10844 88.58388 87.97572 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6238 nv = 96 ne = 84 npr = 50801 no. pairs analyzed = 50801 no. exposed pairs = 4131 no. arc points = 30474 no. surface atoms = 1358 nbur = 1312 mkacc time = 8.9999996E-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 = 1.484000 m= 350 mr = 2667 m= 3 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3040 ## 319 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7768 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4492804E-09 1.4830194E-09 midg,1,midg; midg,igrid,midg -9.8148700E-10 2.8890683E-09 1,midg,midg; igrid,midg,midg 4.0801895E-09 4.4410015E-10 gauss-seidel spectral radius is 0.9847445 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 09:44:52 rms-change max change #iterations 8.9418083E-02 15.84087 at 10iterations 6.9280728E-03 1.170230 at 20iterations 5.5262534E-04 9.1493607E-02 at 30iterations 4.5680295E-05 7.1458817E-03 at 40iterations 5.0115086E-06 7.2479248E-04 at 50iterations finished qdiffx linear iterations at : 09:44:55 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 5.0115086E-06 7.2479248E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 09:44:56 3.462u 0.164s 0:03.93 92.1% 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 09:44:56 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 = 2670 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: 1.745155 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): -17.50900 34.31500 ymin,ymax (A): -61.68100 -2.594000 zmin,zma (A): -0.4859999 60.71200 x,y,z range (A): 51.82400 59.08700 61.19800 scale (grids/A): 1.745155 object centre (A): 8.402999 -32.13750 30.11300 number of atom coordinates read : 2670 total number of charged atoms : 2525 net assigned charge : 7.000017 assigned positive charge : 389.4982 centred at (gu) : 84.17857 86.09898 84.03214 assigned negative charge : -382.4985 centred at (gu) : 84.32496 85.75140 83.92709 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 66400 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30474 grid for indexing accessible points = 1.400000 m= 21560 mr = 39893 m= 3073 mr = 13559 m= 122 mr = 1414 m= 3 mr = 10 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 0.3600000 number of dielectric boundary points 36282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 220 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19638 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) : 0.5817184 object centre at (A) : 8.402999 -32.13750 30.11300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2601464E-03 2.4451418E-03 midg,1,midg; midg,igrid,midg 2.3603402E-02 3.1668749E-02 1,midg,midg; igrid,midg,midg 5.0788377E-03 1.6715418E-03 gauss-seidel spectral radius is 0.9984151 estimated iterations to convergence 199 setup time was (sec) 0.5800000 now iterating at: 09:44:57 rms-change max change #iterations 3.532228 180.2984 at 10iterations 1.544915 58.45308 at 20iterations 0.6812580 24.73227 at 30iterations 0.2988111 10.19932 at 40iterations 0.1308988 5.357271 at 50iterations 5.7712235E-02 2.080095 at 60iterations 2.5407813E-02 0.9598637 at 70iterations 1.1140289E-02 0.3937893 at 80iterations 4.8993411E-03 0.1792717 at 90iterations 2.1658952E-03 7.6082230E-02 at 100iterations 9.5058966E-04 3.4788132E-02 at 110iterations 4.2023754E-04 1.4038086E-02 at 120iterations finished qdiffx linear iterations at : 09:45:04 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 4.2023754E-04 1.4038086E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 09:45:05 7.940u 0.180s 0:08.61 94.3% 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 09:45:05 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 = 2670 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: 2.617733 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): -17.50900 34.31500 ymin,ymax (A): -61.68100 -2.594000 zmin,zma (A): -0.4859999 60.71200 x,y,z range (A): 51.82400 59.08700 61.19800 scale (grids/A): 2.617733 object centre (A): 8.402999 -32.13750 30.11300 number of atom coordinates read : 2670 total number of charged atoms : 2525 net assigned charge : 7.000017 assigned positive charge : 389.4982 centred at (gu) : 81.26771 84.14844 81.04813 assigned negative charge : -382.4985 centred at (gu) : 81.48746 83.62708 80.89056 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 153125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30474 grid for indexing accessible points = 1.400000 m= 69632 mr = 98717 m= 23578 mr = 51292 m= 5004 mr = 16718 m= 464 mr = 3013 m= 20 mr = 195 m= 0 mr = 4 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 81884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 20193 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) : 1.745155 object centre at (A) : 8.402999 -32.13750 30.11300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2131716 1.3751532E-02 midg,1,midg; midg,igrid,midg 0.4586180 0.3517650 1,midg,midg; igrid,midg,midg -4.5298170E-02 1.1034355E-02 gauss-seidel spectral radius is 0.9992261 estimated iterations to convergence 284 setup time was (sec) 1.090000 now iterating at: 09:45:06 rms-change max change #iterations 9.050962 304.7532 at 10iterations 5.380217 151.9163 at 20iterations 3.141124 76.12176 at 30iterations 1.826195 44.40052 at 40iterations 1.053170 32.74954 at 50iterations 0.6056735 14.03096 at 60iterations 0.3472160 8.080160 at 70iterations 0.1987045 4.185452 at 80iterations 0.1133863 2.410322 at 90iterations 6.4671338E-02 1.354361 at 100iterations 3.6830280E-02 0.7902527 at 110iterations 2.0973157E-02 0.4689827 at 120iterations 1.1892826E-02 0.2417488 at 130iterations 6.7792265E-03 0.1412678 at 140iterations 3.8397959E-03 7.6303482E-02 at 150iterations 2.1757642E-03 4.2614698E-02 at 160iterations 1.2357873E-03 2.2487640E-02 at 170iterations 7.0123718E-04 1.5072823E-02 at 180iterations finished qdiffx linear iterations at : 09:45:17 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 7.0123718E-04 1.5072823E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 09:45:18 12.798u 0.222s 0:13.31 97.7% 0+0k 0+0io 0pf+0w