Sat Oct 15 13:00:11 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 Sat Oct 15 2011 at 13:00:12 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 !!! WARNING: HIR 41 has a net charge of 0.5140 !!! WARNING: SEP 187 has a net charge of -0.4750 !!! WARNING: GLM 214 has a net charge of -0.0940 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: 0.6449626 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): -4.375000 46.35500 ymin,ymax (A): 10.22200 56.37500 zmin,zma (A): 10.16400 65.36100 x,y,z range (A): 50.73000 46.15300 55.19700 scale (grids/A): 0.6449626 object centre (A): 20.99000 33.29850 37.76250 number of atom coordinates read : 2752 total number of charged atoms : 2382 net assigned charge : 7.945018 assigned positive charge : 382.3320 centred at (gu) : 89.25157 91.36687 89.95853 assigned negative charge : -374.3878 centred at (gu) : 89.16376 91.28848 89.82573 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7131 nv = 96 ne = 84 npr = 50572 no. pairs analyzed = 50572 no. exposed pairs = 3187 no. arc points = 22492 no. surface atoms = 1062 nbur = 1690 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 3881 m= 4 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0798129E-09 2.9809598E-08 midg,1,midg; midg,igrid,midg 2.4792541E-09 3.1047843E-08 1,midg,midg; igrid,midg,midg 2.0729911E-09 2.0887988E-08 gauss-seidel spectral radius is 0.9875396 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 13:00:12 rms-change max change #iterations 0.1484049 23.91677 at 10iterations 1.5033385E-02 2.065338 at 20iterations 1.5175717E-03 0.2200890 at 30iterations 1.5385549E-04 2.3242950E-02 at 40iterations 1.5296389E-05 2.0465851E-03 at 50iterations finished qdiffx linear iterations at : 13:00:15 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.5296389E-05 2.0465851E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 13:00:15 3.493u 0.188s 0:03.95 92.9% 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 Sat Oct 15 2011 at 13:00:16 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 !!! WARNING: HIR 41 has a net charge of 0.5140 !!! WARNING: SEP 187 has a net charge of -0.4750 !!! WARNING: GLM 214 has a net charge of -0.0940 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: 1.934888 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): -4.375000 46.35500 ymin,ymax (A): 10.22200 56.37500 zmin,zma (A): 10.16400 65.36100 x,y,z range (A): 50.73000 46.15300 55.19700 scale (grids/A): 1.934888 object centre (A): 20.99000 33.29850 37.76250 number of atom coordinates read : 2752 total number of charged atoms : 2382 net assigned charge : 7.945018 assigned positive charge : 382.3320 centred at (gu) : 87.75407 94.10017 89.87510 assigned negative charge : -374.3878 centred at (gu) : 87.49130 93.86529 89.47705 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76828 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22492 grid for indexing accessible points = 1.400000 m= 27511 mr = 53190 m= 4211 mr = 19680 m= 241 mr = 2324 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 33528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 18618 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) : 0.6449626 object centre at (A) : 20.99000 33.29850 37.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4287952E-02 4.7723584E-02 midg,1,midg; midg,igrid,midg -1.7155848E-02 2.5172944E-03 1,midg,midg; igrid,midg,midg 2.3498625E-02 4.4714365E-02 gauss-seidel spectral radius is 0.9986753 estimated iterations to convergence 218 setup time was (sec) 0.6100000 now iterating at: 13:00:16 rms-change max change #iterations 4.295497 174.2952 at 10iterations 2.026533 73.02078 at 20iterations 0.9574544 31.47785 at 30iterations 0.4546043 14.17570 at 40iterations 0.2155894 6.970945 at 50iterations 0.1016664 3.021194 at 60iterations 4.8315175E-02 1.441325 at 70iterations 2.2898465E-02 0.7864761 at 80iterations 1.0844306E-02 0.3608980 at 90iterations 5.1508234E-03 0.1569214 at 100iterations 2.4410852E-03 7.6977730E-02 at 110iterations 1.1578560E-03 3.7262917E-02 at 120iterations finished qdiffx linear iterations at : 13:00:24 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 1.1578560E-03 3.7262917E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 13:00:24 8.110u 0.212s 0:08.62 96.5% 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 15 2011 at 13:00:24 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 !!! WARNING: HIR 41 has a net charge of 0.5140 !!! WARNING: SEP 187 has a net charge of -0.4750 !!! WARNING: GLM 214 has a net charge of -0.0940 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: 2.902332 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): -4.375000 46.35500 ymin,ymax (A): 10.22200 56.37500 zmin,zma (A): 10.16400 65.36100 x,y,z range (A): 50.73000 46.15300 55.19700 scale (grids/A): 2.902332 object centre (A): 20.99000 33.29850 37.76250 number of atom coordinates read : 2752 total number of charged atoms : 2382 net assigned charge : 7.945018 assigned positive charge : 382.3320 centred at (gu) : 86.63100 96.15011 89.81252 assigned negative charge : -374.3878 centred at (gu) : 86.23689 95.79801 89.21539 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 177679 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22492 grid for indexing accessible points = 1.400000 m= 89326 mr = 129199 m= 31691 mr = 71970 m= 7202 mr = 24518 m= 1016 mr = 5027 m= 67 mr = 564 m= 1 mr = 27 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 75678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19041 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) : 1.934888 object centre at (A) : 20.99000 33.29850 37.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2515766E-03 0.3241566 midg,1,midg; midg,igrid,midg -0.1581653 1.7753990E-02 1,midg,midg; igrid,midg,midg 0.1780858 0.4754719 gauss-seidel spectral radius is 0.9992676 estimated iterations to convergence 292 setup time was (sec) 1.230000 now iterating at: 13:00:26 rms-change max change #iterations 10.05076 445.4617 at 10iterations 5.909128 183.7418 at 20iterations 3.455297 94.45511 at 30iterations 2.017076 57.49708 at 40iterations 1.174971 21.88765 at 50iterations 0.6840612 12.70612 at 60iterations 0.3961360 7.258015 at 70iterations 0.2299021 4.212837 at 80iterations 0.1329590 2.460651 at 90iterations 7.7011853E-02 1.416037 at 100iterations 4.4491384E-02 0.8505688 at 110iterations 2.5712093E-02 0.5146710 at 120iterations 1.4843840E-02 0.2681897 at 130iterations 8.5936645E-03 0.1696930 at 140iterations 4.9529788E-03 0.1042700 at 150iterations 2.8690954E-03 5.2652359E-02 at 160iterations 1.6637080E-03 2.9727936E-02 at 170iterations 9.6528832E-04 1.8215179E-02 at 180iterations finished qdiffx linear iterations at : 13:00:38 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 9.6528832E-04 1.8215179E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.32000 DelPhi exited at 13:00:38 13.321u 0.240s 0:13.87 97.7% 0+0k 0+0io 0pf+0w