Mon Oct 10 19:32:55 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+sph2.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 = amb2.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 19:32:55 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 0.6794541 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): -17.10100 35.29400 ymin,ymax (A): -10.16600 37.87400 zmin,zma (A): -2.312000 49.62400 x,y,z range (A): 52.39500 48.04000 51.93600 scale (grids/A): 0.6794541 object centre (A): 9.096501 13.85400 23.65600 number of atom coordinates read : 2420 total number of charged atoms : 2284 net assigned charge : 3.014009 assigned positive charge : 363.9348 centred at (gu) : 92.36047 91.30743 90.83842 assigned negative charge : -360.9215 centred at (gu) : 92.26218 91.51525 90.90811 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7773 nv = 96 ne = 84 npr = 48092 no. pairs analyzed = 48092 no. exposed pairs = 3265 no. arc points = 22565 no. surface atoms = 1087 nbur = 1333 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4187 m= 5 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3500000 number of dielectric boundary points 4002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2083 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8745 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8357528E-08 -9.3000807E-09 midg,1,midg; midg,igrid,midg 5.6209885E-08 -6.5651136E-08 1,midg,midg; igrid,midg,midg -9.8468016E-09 6.8174792E-08 gauss-seidel spectral radius is 0.9887599 estimated iterations to convergence 77 setup time was (sec) 0.6300000 now iterating at: 19:32:55 rms-change max change #iterations 0.1779736 23.90835 at 10iterations 2.0171966E-02 2.709648 at 20iterations 2.4660255E-03 0.3004150 at 30iterations 3.9422492E-04 5.9872627E-02 at 40iterations 1.0456611E-04 1.6348839E-02 at 50iterations finished qdiffx linear iterations at : 19:32:59 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 1.0456611E-04 1.6348839E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 19:32:59 4.030u 0.290s 0:04.83 89.4% 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 19:32:59 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 !!! WARNING: HIR 257 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.038362 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): -17.10100 35.29400 ymin,ymax (A): -10.16600 37.87400 zmin,zma (A): -2.312000 49.62400 x,y,z range (A): 52.39500 48.04000 51.93600 scale (grids/A): 2.038362 object centre (A): 9.096501 13.85400 23.65600 number of atom coordinates read : 2420 total number of charged atoms : 2284 net assigned charge : 3.014009 assigned positive charge : 363.9348 centred at (gu) : 97.08076 93.92176 92.51492 assigned negative charge : -360.9215 centred at (gu) : 96.78629 94.54558 92.72432 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 81977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22565 grid for indexing accessible points = 1.400000 m= 32795 mr = 56328 m= 6780 mr = 24163 m= 663 mr = 4396 m= 21 mr = 313 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1082 time to turn everything in is 0.7000000 number of dielectric boundary points 37033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 18075 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) : 0.6794541 object centre at (A) : 9.096501 13.85400 23.65600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5741477E-02 2.2329383E-02 midg,1,midg; midg,igrid,midg 3.8951911E-02 -5.8811059E-04 1,midg,midg; igrid,midg,midg -9.3264692E-03 2.1415226E-02 gauss-seidel spectral radius is 0.9987896 estimated iterations to convergence 228 setup time was (sec) 1.000000 now iterating at: 19:33:01 rms-change max change #iterations 4.717091 214.4697 at 10iterations 2.292106 78.31223 at 20iterations 1.121828 34.53243 at 30iterations 0.5487373 15.84514 at 40iterations 0.2684681 8.378435 at 50iterations 0.1316094 3.900746 at 60iterations 6.4390011E-02 1.959557 at 70iterations 3.1530701E-02 0.9577656 at 80iterations 1.5444823E-02 0.5317307 at 90iterations 7.5826962E-03 0.2280273 at 100iterations 3.7220709E-03 0.1067009 at 110iterations 1.8385433E-03 5.5633545E-02 at 120iterations finished qdiffx linear iterations at : 19:33:07 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 1.8385433E-03 5.5633545E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 19:33:09 7.705u 0.263s 0:09.37 84.9% 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 19:33:09 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 3.057544 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): -17.10100 35.29400 ymin,ymax (A): -10.16600 37.87400 zmin,zma (A): -2.312000 49.62400 x,y,z range (A): 52.39500 48.04000 51.93600 scale (grids/A): 3.057544 object centre (A): 9.096501 13.85400 23.65600 number of atom coordinates read : 2420 total number of charged atoms : 2284 net assigned charge : 3.014009 assigned positive charge : 363.9348 centred at (gu) : 100.6211 95.88241 93.77229 assigned negative charge : -360.9215 centred at (gu) : 100.1794 96.81841 94.08638 start vw surface at 0.1700000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 189180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22565 grid for indexing accessible points = 1.400000 m= 100476 mr = 136440 m= 42252 mr = 81720 m= 12902 mr = 34249 m= 2617 mr = 9813 m= 296 mr = 1832 m= 9 mr = 155 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 3419 time to turn everything in is 1.590000 number of dielectric boundary points 83524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 18272 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) : 2.038362 object centre at (A) : 9.096501 13.85400 23.65600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4247972 0.7365674 midg,1,midg; midg,igrid,midg 0.3009256 0.2631538 1,midg,midg; igrid,midg,midg -1.5977619E-02 0.1235645 gauss-seidel spectral radius is 0.9993016 estimated iterations to convergence 299 setup time was (sec) 1.910000 now iterating at: 19:33:11 rms-change max change #iterations 10.86443 488.6937 at 10iterations 6.511508 147.6650 at 20iterations 3.873754 74.37383 at 30iterations 2.299561 47.11606 at 40iterations 1.358640 30.82681 at 50iterations 0.8014174 14.75217 at 60iterations 0.4722990 8.172276 at 70iterations 0.2773675 4.832791 at 80iterations 0.1629204 2.698611 at 90iterations 9.5468625E-02 1.576227 at 100iterations 5.6017868E-02 0.9613743 at 110iterations 3.2848537E-02 0.5590801 at 120iterations 1.9201400E-02 0.3359661 at 130iterations 1.1240366E-02 0.1864710 at 140iterations 6.5776333E-03 0.1154938 at 150iterations 3.8484146E-03 6.3277721E-02 at 160iterations 2.2527340E-03 3.8780212E-02 at 170iterations 1.3282698E-03 2.3193359E-02 at 180iterations finished qdiffx linear iterations at : 19:33:22 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 1.3282698E-03 2.3193359E-02 energy calculations done at 12.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 19:33:22 12.624u 0.243s 0:13.31 96.6% 0+0k 0+0io 0pf+0w