Sun Oct 9 05:27:23 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 Sun Oct 9 2011 at 05:27:23 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 !!! WARNING: SEP 415 has a net charge of -0.4750 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: 0.6565238 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): 31.65000 77.93501 ymin,ymax (A): -2.352000 51.87300 zmin,zma (A): -11.63800 30.16000 x,y,z range (A): 46.28500 54.22500 41.79800 scale (grids/A): 0.6565238 object centre (A): 54.79250 24.76050 9.261000 number of atom coordinates read : 2209 total number of charged atoms : 2051 net assigned charge : 2.5013626E-02 assigned positive charge : 298.6952 centred at (gu) : 90.77729 90.27114 90.18665 assigned negative charge : -298.6704 centred at (gu) : 90.81916 90.34782 90.27713 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6438 nv = 96 ne = 84 npr = 47340 no. pairs analyzed = 47340 no. exposed pairs = 2785 no. arc points = 19817 no. surface atoms = 952 nbur = 1257 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 409 mr = 3391 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1659 ## 87 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7378 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2157736E-08 -1.3046068E-08 midg,1,midg; midg,igrid,midg 1.0161545E-08 -1.1213076E-08 1,midg,midg; igrid,midg,midg 5.0711675E-09 -6.7044721E-09 gauss-seidel spectral radius is 0.9879485 estimated iterations to convergence 74 setup time was (sec) 0.6000000 now iterating at: 05:27:24 rms-change max change #iterations 0.1439729 23.56935 at 10iterations 1.4691025E-02 2.260378 at 20iterations 1.6613284E-03 0.2402420 at 30iterations 2.5128922E-04 4.1234970E-02 at 40iterations 6.4351436E-05 9.8842978E-03 at 50iterations finished qdiffx linear iterations at : 05:27:28 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 6.4351436E-05 9.8842978E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 05:27:28 4.051u 0.248s 0:04.56 94.0% 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 05:27:28 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 !!! WARNING: SEP 415 has a net charge of -0.4750 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: 1.969571 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): 31.65000 77.93501 ymin,ymax (A): -2.352000 51.87300 zmin,zma (A): -11.63800 30.16000 x,y,z range (A): 46.28500 54.22500 41.79800 scale (grids/A): 1.969571 object centre (A): 54.79250 24.76050 9.261000 number of atom coordinates read : 2209 total number of charged atoms : 2051 net assigned charge : 2.5013626E-02 assigned positive charge : 298.6952 centred at (gu) : 92.33197 90.81363 90.55992 assigned negative charge : -298.6704 centred at (gu) : 92.45781 91.04380 90.83155 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19817 grid for indexing accessible points = 1.400000 m= 25337 mr = 46617 m= 4556 mr = 18332 m= 268 mr = 2854 m= 3 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 231 time to turn everything in is 0.6400000 number of dielectric boundary points 31357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 16245 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) : 0.6565238 object centre at (A) : 54.79250 24.76050 9.261000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5853804E-02 9.2399423E-04 midg,1,midg; midg,igrid,midg -4.7971033E-03 -3.4717996E-02 1,midg,midg; igrid,midg,midg 5.5171321E-03 -1.9068628E-03 gauss-seidel spectral radius is 0.9986933 estimated iterations to convergence 219 setup time was (sec) 0.9200000 now iterating at: 05:27:29 rms-change max change #iterations 3.972438 163.1220 at 10iterations 1.891582 70.33749 at 20iterations 0.8983181 31.36968 at 30iterations 0.4271562 14.52498 at 40iterations 0.2036993 6.571371 at 50iterations 9.7184800E-02 3.297829 at 60iterations 4.6141572E-02 1.625597 at 70iterations 2.2018610E-02 0.7038994 at 80iterations 1.0522821E-02 0.3460073 at 90iterations 5.0284532E-03 0.1814036 at 100iterations 2.4224685E-03 7.5672150E-02 at 110iterations 1.1759285E-03 4.0818214E-02 at 120iterations finished qdiffx linear iterations at : 05:27:37 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 1.1759285E-03 4.0818214E-02 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.340000 DelPhi exited at 05:27:38 9.345u 0.298s 0:09.91 97.1% 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 Sun Oct 9 2011 at 05:27:38 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 !!! WARNING: SEP 415 has a net charge of -0.4750 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: 2.954357 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): 31.65000 77.93501 ymin,ymax (A): -2.352000 51.87300 zmin,zma (A): -11.63800 30.16000 x,y,z range (A): 46.28500 54.22500 41.79800 scale (grids/A): 2.954357 object centre (A): 54.79250 24.76050 9.261000 number of atom coordinates read : 2209 total number of charged atoms : 2051 net assigned charge : 2.5013626E-02 assigned positive charge : 298.6952 centred at (gu) : 93.49800 91.22043 90.83982 assigned negative charge : -298.6704 centred at (gu) : 93.68679 91.56570 91.24752 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 159643 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19817 grid for indexing accessible points = 1.400000 m= 79728 mr = 113379 m= 31054 mr = 64300 m= 8253 mr = 24535 m= 1226 mr = 6273 m= 52 mr = 772 m= 0 mr = 10 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 824 time to turn everything in is 1.640000 number of dielectric boundary points 70687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 16407 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) : 1.969571 object centre at (A) : 54.79250 24.76050 9.261000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1534134 2.5508117E-02 midg,1,midg; midg,igrid,midg 2.3127411E-02 -0.2500289 1,midg,midg; igrid,midg,midg 4.1829620E-02 -1.1805946E-02 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.970000 now iterating at: 05:27:40 rms-change max change #iterations 8.994840 487.6880 at 10iterations 5.191640 122.7971 at 20iterations 2.992847 60.17072 at 30iterations 1.726373 33.86679 at 40iterations 0.9944345 19.09944 at 50iterations 0.5734019 10.78373 at 60iterations 0.3299010 5.834903 at 70iterations 0.1900080 3.397745 at 80iterations 0.1095779 1.952530 at 90iterations 6.3233912E-02 1.157582 at 100iterations 3.6307510E-02 0.6663437 at 110iterations 2.0943224E-02 0.3902180 at 120iterations 1.2073659E-02 0.2182717 at 130iterations 6.9797672E-03 0.1265602 at 140iterations 4.0394170E-03 7.4190140E-02 at 150iterations 2.3568484E-03 4.3807983E-02 at 160iterations 1.3767150E-03 2.4291992E-02 at 170iterations 8.2308217E-04 1.4830112E-02 at 180iterations finished qdiffx linear iterations at : 05:27:54 total time elapsed so far: 15.52000 # loops : 180 mean,max change (kT/e) : 8.2308217E-04 1.4830112E-02 energy calculations done at 15.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.69000 DelPhi exited at 05:27:54 15.695u 0.304s 0:16.26 98.3% 0+0k 0+0io 0pf+0w