Sun Oct 9 06:52:20 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 Sun Oct 9 2011 at 06:52:20 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 0.7274362 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): -25.93800 17.51700 ymin,ymax (A): -21.44600 17.84100 zmin,zma (A): -19.55900 29.38000 x,y,z range (A): 43.45500 39.28700 48.93900 scale (grids/A): 0.7274362 object centre (A): -4.210500 -1.802500 4.910500 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 90.42987 90.67316 90.79038 assigned negative charge : -302.1561 centred at (gu) : 90.30855 90.81638 90.94975 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7277 nv = 96 ne = 84 npr = 41798 no. pairs analyzed = 41798 no. exposed pairs = 2483 no. arc points = 17535 no. surface atoms = 838 nbur = 1163 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 487 mr = 4067 m= 5 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 89 time to turn everything in is 0.2600000 number of dielectric boundary points 3604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1482 ## 100 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7824 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1896039E-08 -1.7617462E-07 midg,1,midg; midg,igrid,midg 6.3427841E-08 -1.5820541E-07 1,midg,midg; igrid,midg,midg -1.1268008E-07 6.1936333E-08 gauss-seidel spectral radius is 0.9901432 estimated iterations to convergence 82 setup time was (sec) 0.4900000 now iterating at: 06:52:21 rms-change max change #iterations 0.2304774 30.96486 at 10iterations 2.9702164E-02 4.318461 at 20iterations 3.8200286E-03 0.5344362 at 30iterations 4.9832149E-04 7.1723938E-02 at 40iterations 6.5274638E-05 8.2778931E-03 at 50iterations finished qdiffx linear iterations at : 06:52:23 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 6.5274638E-05 8.2778931E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 06:52:23 3.056u 0.154s 0:03.48 91.9% 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 Sun Oct 9 2011 at 06:52:23 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 2.182309 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): -25.93800 17.51700 ymin,ymax (A): -21.44600 17.84100 zmin,zma (A): -19.55900 29.38000 x,y,z range (A): 43.45500 39.28700 48.93900 scale (grids/A): 2.182309 object centre (A): -4.210500 -1.802500 4.910500 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 91.28979 92.01933 92.37113 assigned negative charge : -302.1561 centred at (gu) : 90.92575 92.44927 92.84941 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 76518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17535 grid for indexing accessible points = 1.400000 m= 29938 mr = 53097 m= 6164 mr = 22702 m= 642 mr = 4298 m= 11 mr = 360 m= 0 mr = 1 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2191 time to turn everything in is 0.5400000 number of dielectric boundary points 32815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 14827 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) : 0.7274362 object centre at (A) : -4.210500 -1.802500 4.910500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6009808E-02 -5.7253025E-02 midg,1,midg; midg,igrid,midg 2.9430870E-02 -1.0898237E-02 1,midg,midg; igrid,midg,midg -2.1955701E-02 1.1118499E-03 gauss-seidel spectral radius is 0.9988844 estimated iterations to convergence 237 setup time was (sec) 0.8000000 now iterating at: 06:52:24 rms-change max change #iterations 4.822287 197.7796 at 10iterations 2.417123 77.41819 at 20iterations 1.216766 38.02310 at 30iterations 0.6150980 18.87100 at 40iterations 0.3085386 8.561028 at 50iterations 0.1553600 5.114047 at 60iterations 7.8103758E-02 2.455742 at 70iterations 3.9361190E-02 1.206133 at 80iterations 1.9816417E-02 0.6016216 at 90iterations 9.9686310E-03 0.2792091 at 100iterations 5.0338022E-03 0.1458893 at 110iterations 2.5300481E-03 6.8913937E-02 at 120iterations finished qdiffx linear iterations at : 06:52:30 total time elapsed so far: 6.690000 # loops : 120 mean,max change (kT/e) : 2.5300481E-03 6.8913937E-02 energy calculations done at 6.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 06:52:31 6.863u 0.174s 0:07.30 96.3% 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 Sun Oct 9 2011 at 06:52:31 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 3.273463 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): -25.93800 17.51700 ymin,ymax (A): -21.44600 17.84100 zmin,zma (A): -19.55900 29.38000 x,y,z range (A): 43.45500 39.28700 48.93900 scale (grids/A): 3.273463 object centre (A): -4.210500 -1.802500 4.910500 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 91.93465 93.02900 93.55676 assigned negative charge : -302.1561 centred at (gu) : 91.38857 93.67387 94.27412 start vw surface at 0.1400000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 176292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17535 grid for indexing accessible points = 1.400000 m= 93191 mr = 127984 m= 38263 mr = 77232 m= 11768 mr = 31679 m= 2622 mr = 9318 m= 341 mr = 2002 m= 11 mr = 209 m= 0 mr = 2 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 7229 time to turn everything in is 1.720000 number of dielectric boundary points 74062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 14896 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) : 2.182309 object centre at (A) : -4.210500 -1.802500 4.910500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1556791 -0.3540252 midg,1,midg; midg,igrid,midg 0.2766576 -2.5117455E-02 1,midg,midg; igrid,midg,midg -0.1173673 -0.1035323 gauss-seidel spectral radius is 0.9993047 estimated iterations to convergence 299 setup time was (sec) 2.000000 now iterating at: 06:52:33 rms-change max change #iterations 10.44590 371.0533 at 10iterations 6.094313 140.5231 at 20iterations 3.549359 64.88181 at 30iterations 2.072911 35.89679 at 40iterations 1.213258 26.12372 at 50iterations 0.7086332 12.30243 at 60iterations 0.4134995 7.770428 at 70iterations 0.2413214 5.393114 at 80iterations 0.1407139 2.500122 at 90iterations 8.2169965E-02 1.492889 at 100iterations 4.7977474E-02 0.8042876 at 110iterations 2.7952056E-02 0.4969330 at 120iterations 1.6290028E-02 0.2851685 at 130iterations 9.5568253E-03 0.1606445 at 140iterations 5.5730753E-03 0.1012497 at 150iterations 3.2502243E-03 5.3310394E-02 at 160iterations 1.8954466E-03 3.4404755E-02 at 170iterations 1.1067999E-03 1.8012047E-02 at 180iterations finished qdiffx linear iterations at : 06:52:42 total time elapsed so far: 11.43000 # loops : 180 mean,max change (kT/e) : 1.1067999E-03 1.8012047E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.61000 DelPhi exited at 06:52:43 11.609u 0.176s 0:12.06 97.5% 0+0k 0+0io 0pf+0w