Mon Oct 10 10:21:05 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 10:21:05 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 = 2895 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5624812 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): 17.48200 74.33300 ymin,ymax (A): -44.12800 5.781000 zmin,zma (A): 7.661000 70.95200 x,y,z range (A): 56.85100 49.90900 63.29100 scale (grids/A): 0.5624812 object centre (A): 45.90750 -19.17350 39.30650 number of atom coordinates read : 2895 total number of charged atoms : 2745 net assigned charge : 9.000024 assigned positive charge : 423.6619 centred at (gu) : 92.15466 89.33210 89.24801 assigned negative charge : -414.6623 centred at (gu) : 92.40891 89.40007 89.18815 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6192 nv = 96 ne = 84 npr = 55774 no. pairs analyzed = 55774 no. exposed pairs = 4348 no. arc points = 31815 no. surface atoms = 1447 nbur = 1448 mkacc time = 0.1300000 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 = 1.540000 m= 274 mr = 2706 m= 1 mr = 15 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 3746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3144 ## 399 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7889 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1979798E-10 1.4901326E-09 midg,1,midg; midg,igrid,midg 2.1946744E-09 3.0350250E-10 1,midg,midg; igrid,midg,midg 2.3173756E-09 -3.1578957E-09 gauss-seidel spectral radius is 0.9837081 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 10:21:06 rms-change max change #iterations 7.8703865E-02 13.50539 at 10iterations 5.6564189E-03 1.037270 at 20iterations 3.9739563E-04 6.6255569E-02 at 30iterations 2.9564932E-05 4.6691895E-03 at 40iterations 2.5082859E-06 4.6586990E-04 at 50iterations finished qdiffx linear iterations at : 10:21:08 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.5082859E-06 4.6586990E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 10:21:09 3.456u 0.155s 0:03.98 90.4% 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 Mon Oct 10 2011 at 10:21:09 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 = 2895 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.687444 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): 17.48200 74.33300 ymin,ymax (A): -44.12800 5.781000 zmin,zma (A): 7.661000 70.95200 x,y,z range (A): 56.85100 49.90900 63.29100 scale (grids/A): 1.687444 object centre (A): 45.90750 -19.17350 39.30650 number of atom coordinates read : 2895 total number of charged atoms : 2745 net assigned charge : 9.000024 assigned positive charge : 423.6619 centred at (gu) : 96.46359 87.99590 87.74356 assigned negative charge : -414.6623 centred at (gu) : 97.22666 88.19995 87.56405 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 67105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31815 grid for indexing accessible points = 1.400000 m= 20085 mr = 41063 m= 2245 mr = 12497 m= 83 mr = 939 m= 0 mr = 6 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 35013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 21140 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) : 0.5624812 object centre at (A) : 45.90750 -19.17350 39.30650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3453478E-02 1.9126534E-02 midg,1,midg; midg,igrid,midg 1.0742423E-02 1.0838611E-02 1,midg,midg; igrid,midg,midg 2.4832897E-02 -1.2515378E-03 gauss-seidel spectral radius is 0.9983216 estimated iterations to convergence 194 setup time was (sec) 0.8000000 now iterating at: 10:21:10 rms-change max change #iterations 3.418795 152.7183 at 10iterations 1.464284 54.76854 at 20iterations 0.6290910 22.76472 at 30iterations 0.2703404 9.837962 at 40iterations 0.1164588 4.293679 at 50iterations 4.9761526E-02 1.669552 at 60iterations 2.1357158E-02 0.7487010 at 70iterations 9.2358626E-03 0.3578730 at 80iterations 3.9696428E-03 0.1523294 at 90iterations 1.7025529E-03 5.8204651E-02 at 100iterations 7.3534489E-04 2.7479172E-02 at 110iterations 3.1530825E-04 1.1234283E-02 at 120iterations finished qdiffx linear iterations at : 10:21:17 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 3.1530825E-04 1.1234283E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 10:21:17 7.694u 0.172s 0:08.12 96.7% 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 10:21:17 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 = 2895 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.531165 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): 17.48200 74.33300 ymin,ymax (A): -44.12800 5.781000 zmin,zma (A): 7.661000 70.95200 x,y,z range (A): 56.85100 49.90900 63.29100 scale (grids/A): 2.531165 object centre (A): 45.90750 -19.17350 39.30650 number of atom coordinates read : 2895 total number of charged atoms : 2745 net assigned charge : 9.000024 assigned positive charge : 423.6619 centred at (gu) : 99.69540 86.99371 86.61516 assigned negative charge : -414.6623 centred at (gu) : 100.8398 87.29996 86.34604 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 155109 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31815 grid for indexing accessible points = 1.400000 m= 67868 mr = 101249 m= 19917 mr = 50241 m= 3418 mr = 13929 m= 277 mr = 2016 m= 8 mr = 99 m= 0 mr = 2 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 79061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 21949 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) : 1.687444 object centre at (A) : 45.90750 -19.17350 39.30650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6282670 0.3291669 midg,1,midg; midg,igrid,midg 8.6228058E-02 0.1330442 1,midg,midg; igrid,midg,midg 0.3948950 5.3753625E-03 gauss-seidel spectral radius is 0.9991949 estimated iterations to convergence 278 setup time was (sec) 1.530000 now iterating at: 10:21:19 rms-change max change #iterations 8.918388 383.4144 at 10iterations 5.183577 135.3189 at 20iterations 2.979800 104.2591 at 30iterations 1.702145 49.18158 at 40iterations 0.9690958 22.84958 at 50iterations 0.5496723 14.21378 at 60iterations 0.3105098 6.967293 at 70iterations 0.1748185 3.674221 at 80iterations 9.8604023E-02 2.107176 at 90iterations 5.5382378E-02 1.218029 at 100iterations 3.1203793E-02 0.7118554 at 110iterations 1.7503684E-02 0.3851435 at 120iterations 9.8174447E-03 0.1993070 at 130iterations 5.5095800E-03 0.1171770 at 140iterations 3.0924361E-03 6.0037613E-02 at 150iterations 1.7298775E-03 3.8139343E-02 at 160iterations 9.7061077E-04 2.0087719E-02 at 170iterations 5.4495415E-04 1.1389732E-02 at 180iterations finished qdiffx linear iterations at : 10:21:29 total time elapsed so far: 11.90000 # loops : 180 mean,max change (kT/e) : 5.4495415E-04 1.1389732E-02 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 10:21:30 12.099u 0.216s 0:12.58 97.7% 0+0k 0+0io 0pf+0w