Sun Oct 9 07:59:05 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 07:59:05 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 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: 0.6990123 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): 4.547000 49.99200 ymin,ymax (A): -24.75400 26.17500 zmin,zma (A): -19.40800 30.26400 x,y,z range (A): 45.44500 50.92900 49.67200 scale (grids/A): 0.6990123 object centre (A): 27.26950 0.7104998 5.428000 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327990 assigned positive charge : 340.4184 centred at (gu) : 89.96015 91.04075 90.14283 assigned negative charge : -343.7467 centred at (gu) : 89.98566 91.12891 90.24648 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7491 nv = 96 ne = 84 npr = 44933 no. pairs analyzed = 44933 no. exposed pairs = 2927 no. arc points = 20944 no. surface atoms = 966 nbur = 1253 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 534 mr = 4068 m= 6 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.3300000 number of dielectric boundary points 3873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1968 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8264 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3086020E-08 -7.1481423E-08 midg,1,midg; midg,igrid,midg 1.3545272E-08 -7.6731752E-08 1,midg,midg; igrid,midg,midg -1.0984247E-08 -3.3600735E-08 gauss-seidel spectral radius is 0.9893585 estimated iterations to convergence 79 setup time was (sec) 0.6400000 now iterating at: 07:59:05 rms-change max change #iterations 0.2042848 27.55322 at 10iterations 2.4147823E-02 3.045364 at 20iterations 2.8965564E-03 0.4668961 at 30iterations 3.4393228E-04 5.0876617E-02 at 40iterations 4.1253621E-05 5.3863525E-03 at 50iterations finished qdiffx linear iterations at : 07:59:09 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 4.1253621E-05 5.3863525E-03 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 07:59:10 4.376u 0.264s 0:04.90 94.4% 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 Sun Oct 9 2011 at 07:59:10 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 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: 2.097037 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): 4.547000 49.99200 ymin,ymax (A): -24.75400 26.17500 zmin,zma (A): -19.40800 30.26400 x,y,z range (A): 45.44500 50.92900 49.67200 scale (grids/A): 2.097037 object centre (A): 27.26950 0.7104998 5.428000 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327990 assigned positive charge : 340.4184 centred at (gu) : 89.88010 93.12209 90.42793 assigned negative charge : -343.7467 centred at (gu) : 89.95702 93.38655 90.73923 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 78953 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20944 grid for indexing accessible points = 1.400000 m= 31157 mr = 53712 m= 6326 mr = 23130 m= 677 mr = 4251 m= 33 mr = 346 m= 0 mr = 9 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1447 time to turn everything in is 0.7300000 number of dielectric boundary points 35698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 16492 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) : 0.6990123 object centre at (A) : 27.26950 0.7104998 5.428000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5471839E-04 -4.2962793E-02 midg,1,midg; midg,igrid,midg 3.0407904E-02 -4.3828934E-03 1,midg,midg; igrid,midg,midg -3.7759633E-03 -3.3388309E-02 gauss-seidel spectral radius is 0.9988346 estimated iterations to convergence 232 setup time was (sec) 1.070000 now iterating at: 07:59:11 rms-change max change #iterations 4.861048 229.7304 at 10iterations 2.399015 76.77720 at 20iterations 1.188150 38.41549 at 30iterations 0.5884936 18.33560 at 40iterations 0.2915882 9.049244 at 50iterations 0.1446340 4.484703 at 60iterations 7.1609341E-02 2.291161 at 70iterations 3.5433453E-02 1.116882 at 80iterations 1.7547162E-02 0.5201950 at 90iterations 8.7246625E-03 0.2878551 at 100iterations 4.3143597E-03 0.1304264 at 110iterations 2.1460373E-03 6.5126419E-02 at 120iterations finished qdiffx linear iterations at : 07:59:20 total time elapsed so far: 9.930000 # loops : 120 mean,max change (kT/e) : 2.1460373E-03 6.5126419E-02 energy calculations done at 9.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.11000 DelPhi exited at 07:59:20 10.115u 0.319s 0:10.68 97.5% 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 Sun Oct 9 2011 at 07:59:20 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 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: 3.145555 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): 4.547000 49.99200 ymin,ymax (A): -24.75400 26.17500 zmin,zma (A): -19.40800 30.26400 x,y,z range (A): 45.44500 50.92900 49.67200 scale (grids/A): 3.145555 object centre (A): 27.26950 0.7104998 5.428000 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327990 assigned positive charge : 340.4184 centred at (gu) : 89.81993 94.68303 90.64188 assigned negative charge : -343.7467 centred at (gu) : 89.93550 95.07979 91.10886 start vw surface at 0.1500000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 181723 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20944 grid for indexing accessible points = 1.400000 m= 96401 mr = 129631 m= 40069 mr = 79039 m= 12112 mr = 32756 m= 2673 mr = 9426 m= 400 mr = 1907 m= 29 mr = 252 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 4900 time to turn everything in is 2.050000 number of dielectric boundary points 80387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 16615 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) : 2.097037 object centre at (A) : 27.26950 0.7104998 5.428000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0067635E-03 -0.2652611 midg,1,midg; midg,igrid,midg 0.9054825 7.6301098E-02 1,midg,midg; igrid,midg,midg -6.3024163E-02 -0.2845379 gauss-seidel spectral radius is 0.9993040 estimated iterations to convergence 299 setup time was (sec) 2.420000 now iterating at: 07:59:23 rms-change max change #iterations 10.91577 366.4757 at 10iterations 6.425569 135.3210 at 20iterations 3.772338 74.20685 at 30iterations 2.216265 45.69604 at 40iterations 1.301782 24.97744 at 50iterations 0.7635815 13.57619 at 60iterations 0.4479594 7.749786 at 70iterations 0.2626579 4.586070 at 80iterations 0.1534459 2.829594 at 90iterations 8.9748017E-02 1.594810 at 100iterations 5.2452218E-02 0.9289280 at 110iterations 3.0601799E-02 0.5230241 at 120iterations 1.7884789E-02 0.3204727 at 130iterations 1.0460994E-02 0.1731692 at 140iterations 6.1405338E-03 0.1071968 at 150iterations 3.5882795E-03 6.2857613E-02 at 160iterations 2.1040144E-03 3.4679413E-02 at 170iterations 1.2358212E-03 2.4513245E-02 at 180iterations finished qdiffx linear iterations at : 07:59:37 total time elapsed so far: 16.84000 # loops : 180 mean,max change (kT/e) : 1.2358212E-03 2.4513245E-02 energy calculations done at 16.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.01000 DelPhi exited at 07:59:38 17.014u 0.341s 0:17.62 98.4% 0+0k 0+0io 0pf+0w