Sat Oct 8 21:29:09 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 8 2011 at 21:29:09 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: GLM 128 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6455356 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): -28.29000 23.79200 ymin,ymax (A): -27.18000 27.96800 zmin,zma (A): -8.199000 42.62900 x,y,z range (A): 52.08200 55.14800 50.82800 scale (grids/A): 0.6455356 object centre (A): -2.249000 0.3940001 17.21500 number of atom coordinates read : 2622 total number of charged atoms : 2482 net assigned charge : 3.420003 assigned positive charge : 396.8068 centred at (gu) : 92.89655 90.37179 92.48779 assigned negative charge : -393.3874 centred at (gu) : 92.85839 90.36854 92.48042 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7492 nv = 96 ne = 84 npr = 52025 no. pairs analyzed = 52025 no. exposed pairs = 3449 no. arc points = 24487 no. surface atoms = 1146 nbur = 1476 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 4024 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2275 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8823 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7706704E-09 1.0990084E-08 midg,1,midg; midg,igrid,midg 4.7279616E-09 6.4504300E-09 1,midg,midg; igrid,midg,midg 3.0106340E-10 1.9825924E-08 gauss-seidel spectral radius is 0.9875720 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 21:29:10 rms-change max change #iterations 0.1557948 21.40484 at 10iterations 1.5577341E-02 2.433802 at 20iterations 1.6009245E-03 0.2202559 at 30iterations 1.9613715E-04 2.4540424E-02 at 40iterations 4.1196414E-05 5.0477982E-03 at 50iterations finished qdiffx linear iterations at : 21:29:13 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 4.1196414E-05 5.0477982E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 21:29:13 3.365u 0.173s 0:03.83 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 Sat Oct 8 2011 at 21:29:13 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: GLM 128 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.936607 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): -28.29000 23.79200 ymin,ymax (A): -27.18000 27.96800 zmin,zma (A): -8.199000 42.62900 x,y,z range (A): 52.08200 55.14800 50.82800 scale (grids/A): 1.936607 object centre (A): -2.249000 0.3940001 17.21500 number of atom coordinates read : 2622 total number of charged atoms : 2482 net assigned charge : 3.420003 assigned positive charge : 396.8068 centred at (gu) : 98.68904 91.11475 97.46285 assigned negative charge : -393.3874 centred at (gu) : 98.57467 91.10545 97.44086 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 80522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24487 grid for indexing accessible points = 1.400000 m= 28832 mr = 55614 m= 4608 mr = 20459 m= 287 mr = 2739 m= 7 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 366 time to turn everything in is 0.3900000 number of dielectric boundary points 35347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 19523 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) : 0.6455356 object centre at (A) : -2.249000 0.3940001 17.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5136153E-02 -3.7290547E-03 midg,1,midg; midg,igrid,midg 1.8945904E-02 -3.4231152E-02 1,midg,midg; igrid,midg,midg 2.2048555E-02 4.9386104E-03 gauss-seidel spectral radius is 0.9986805 estimated iterations to convergence 218 setup time was (sec) 0.6000000 now iterating at: 21:29:14 rms-change max change #iterations 4.465438 195.5226 at 10iterations 2.118044 78.87522 at 20iterations 1.007131 35.57806 at 30iterations 0.4784338 16.75542 at 40iterations 0.2267473 7.541368 at 50iterations 0.1079336 3.348752 at 60iterations 5.1215749E-02 1.565598 at 70iterations 2.4327448E-02 0.7370619 at 80iterations 1.1540764E-02 0.3964233 at 90iterations 5.4882658E-03 0.1713295 at 100iterations 2.6174078E-03 8.1817627E-02 at 110iterations 1.2449551E-03 3.4833908E-02 at 120iterations finished qdiffx linear iterations at : 21:29:21 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 1.2449551E-03 3.4833908E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 21:29:21 7.797u 0.206s 0:08.26 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 Sat Oct 8 2011 at 21:29:21 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: GLM 128 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.904910 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): -28.29000 23.79200 ymin,ymax (A): -27.18000 27.96800 zmin,zma (A): -8.199000 42.62900 x,y,z range (A): 52.08200 55.14800 50.82800 scale (grids/A): 2.904910 object centre (A): -2.249000 0.3940001 17.21500 number of atom coordinates read : 2622 total number of charged atoms : 2482 net assigned charge : 3.420003 assigned positive charge : 396.8068 centred at (gu) : 103.0334 91.67196 101.1941 assigned negative charge : -393.3874 centred at (gu) : 102.8619 91.65806 101.1611 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 186405 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24487 grid for indexing accessible points = 1.400000 m= 93853 mr = 134900 m= 33176 mr = 75789 m= 8298 mr = 25686 m= 1194 mr = 5992 m= 59 mr = 726 m= 3 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 1201 time to turn everything in is 1.020000 number of dielectric boundary points 79877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 19851 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) : 1.936607 object centre at (A) : -2.249000 0.3940001 17.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1815550 -4.1208755E-02 midg,1,midg; midg,igrid,midg 8.8241212E-02 -1.100832 1,midg,midg; igrid,midg,midg 0.2004869 -6.0938478E-02 gauss-seidel spectral radius is 0.9992821 estimated iterations to convergence 294 setup time was (sec) 1.270000 now iterating at: 21:29:23 rms-change max change #iterations 10.51088 319.7052 at 10iterations 6.258801 162.1054 at 20iterations 3.695914 87.70056 at 30iterations 2.179858 43.71246 at 40iterations 1.281000 27.38520 at 50iterations 0.7476231 14.48045 at 60iterations 0.4377776 9.422527 at 70iterations 0.2553396 4.827542 at 80iterations 0.1486146 2.886539 at 90iterations 8.6484991E-02 1.528051 at 100iterations 5.0262105E-02 0.9376907 at 110iterations 2.9263215E-02 0.4933052 at 120iterations 1.6989730E-02 0.3057556 at 130iterations 9.8760389E-03 0.1671906 at 140iterations 5.7326704E-03 0.1085339 at 150iterations 3.3286836E-03 5.7968140E-02 at 160iterations 1.9317040E-03 3.7301540E-02 at 170iterations 1.1220913E-03 2.0465851E-02 at 180iterations finished qdiffx linear iterations at : 21:29:34 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 1.1220913E-03 2.0465851E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 21:29:35 12.816u 0.199s 0:13.31 97.6% 0+0k 0+0io 0pf+0w