Sun Oct 9 22:43:30 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 22:43:30 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3075 !!! WARNING: HIZ 20 has a net charge of 0.2000 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 679 has a net charge of -0.6000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 778 has a net charge of 1.4000 !!! WARNING: ZN7 779 has a net charge of 1.4000 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: 0.6634859 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): -41.49000 11.63700 ymin,ymax (A): -56.38100 -2.725000 zmin,zma (A): -8.502000 43.80100 x,y,z range (A): 53.12700 53.65600 52.30300 scale (grids/A): 0.6634859 object centre (A): -14.92650 -29.55300 17.64950 number of atom coordinates read : 3075 total number of charged atoms : 3023 net assigned charge : 7.900013 assigned positive charge : 482.4887 centred at (gu) : 89.53375 91.40232 90.63699 assigned negative charge : -474.5901 centred at (gu) : 89.66392 91.48862 90.63136 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 9374 nv = 96 ne = 84 npr = 57958 no. pairs analyzed = 57958 no. exposed pairs = 4268 no. arc points = 30912 no. surface atoms = 1405 nbur = 1670 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 557 mr = 4812 m= 8 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2200000 number of dielectric boundary points 5067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2977 ## 278 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 11177 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8263361E-08 2.6928372E-08 midg,1,midg; midg,igrid,midg 3.3636415E-08 -1.5376420E-09 1,midg,midg; igrid,midg,midg 6.1758513E-08 -1.1311523E-08 gauss-seidel spectral radius is 0.9882843 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 22:43:31 rms-change max change #iterations 0.1924396 51.12900 at 10iterations 2.0517875E-02 5.940338 at 20iterations 2.1910886E-03 0.5877075 at 30iterations 2.3965060E-04 5.2459717E-02 at 40iterations 2.7100683E-05 3.9367676E-03 at 50iterations finished qdiffx linear iterations at : 22:43:34 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 2.7100683E-05 3.9367676E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 22:43:34 3.501u 0.182s 0:04.06 90.6% 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 22:43:34 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3075 !!! WARNING: HIZ 20 has a net charge of 0.2000 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 679 has a net charge of -0.6000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 778 has a net charge of 1.4000 !!! WARNING: ZN7 779 has a net charge of 1.4000 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: 1.990458 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): -41.49000 11.63700 ymin,ymax (A): -56.38100 -2.725000 zmin,zma (A): -8.502000 43.80100 x,y,z range (A): 53.12700 53.65600 52.30300 scale (grids/A): 1.990458 object centre (A): -14.92650 -29.55300 17.64950 number of atom coordinates read : 3075 total number of charged atoms : 3023 net assigned charge : 7.900013 assigned positive charge : 482.4887 centred at (gu) : 88.60028 94.20603 91.91017 assigned negative charge : -474.5901 centred at (gu) : 88.99171 94.46541 91.89346 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 100369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30912 grid for indexing accessible points = 1.400000 m= 36473 mr = 67262 m= 6409 mr = 25817 m= 511 mr = 3780 m= 8 mr = 205 m= 0 mr = 1 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1106 time to turn everything in is 0.4900000 number of dielectric boundary points 46705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 23859 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) : 0.6634859 object centre at (A) : -14.92650 -29.55300 17.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8276774E-03 -1.4642464E-02 midg,1,midg; midg,igrid,midg 4.9567960E-02 8.6704753E-02 1,midg,midg; igrid,midg,midg 4.1487187E-02 6.0827681E-03 gauss-seidel spectral radius is 0.9988111 estimated iterations to convergence 230 setup time was (sec) 0.7200000 now iterating at: 22:43:35 rms-change max change #iterations 5.195175 226.7686 at 10iterations 2.557720 82.15388 at 20iterations 1.250201 35.87309 at 30iterations 0.6154441 16.95616 at 40iterations 0.3026997 8.582294 at 50iterations 0.1490869 4.110660 at 60iterations 7.3143609E-02 1.916788 at 70iterations 3.5996024E-02 0.9912443 at 80iterations 1.7644688E-02 0.4754124 at 90iterations 8.6910753E-03 0.2503510 at 100iterations 4.2797183E-03 0.1176624 at 110iterations 2.1136964E-03 5.8466911E-02 at 120iterations finished qdiffx linear iterations at : 22:43:42 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 2.1136964E-03 5.8466911E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 22:43:43 8.221u 0.193s 0:08.80 95.5% 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 22:43:43 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3075 !!! WARNING: HIZ 20 has a net charge of 0.2000 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 679 has a net charge of -0.6000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 778 has a net charge of 1.4000 !!! WARNING: ZN7 779 has a net charge of 1.4000 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: 2.985687 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): -41.49000 11.63700 ymin,ymax (A): -56.38100 -2.725000 zmin,zma (A): -8.502000 43.80100 x,y,z range (A): 53.12700 53.65600 52.30300 scale (grids/A): 2.985687 object centre (A): -14.92650 -29.55300 17.64950 number of atom coordinates read : 3075 total number of charged atoms : 3023 net assigned charge : 7.900013 assigned positive charge : 482.4887 centred at (gu) : 87.90038 96.30882 92.86502 assigned negative charge : -474.5901 centred at (gu) : 88.48748 96.69804 92.84016 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 231812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30912 grid for indexing accessible points = 1.400000 m= 116382 mr = 163639 m= 43319 mr = 92931 m= 11704 mr = 33652 m= 2160 mr = 8415 m= 215 mr = 1421 m= 6 mr = 117 m= 0 mr = 2 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 3737 time to turn everything in is 1.280000 number of dielectric boundary points 105421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 24172 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) : 1.990458 object centre at (A) : -14.92650 -29.55300 17.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0803404E-03 -0.3109209 midg,1,midg; midg,igrid,midg 0.3146263 0.5389540 1,midg,midg; igrid,midg,midg 0.3948272 0.2241329 gauss-seidel spectral radius is 0.9993345 estimated iterations to convergence 306 setup time was (sec) 1.530000 now iterating at: 22:43:45 rms-change max change #iterations 12.21548 375.7412 at 10iterations 7.446529 211.8022 at 20iterations 4.510846 102.0174 at 30iterations 2.724594 51.92571 at 40iterations 1.636359 29.41331 at 50iterations 0.9827991 18.98697 at 60iterations 0.5869571 10.90391 at 70iterations 0.3509402 5.985339 at 80iterations 0.2088525 3.403381 at 90iterations 0.1241462 1.925095 at 100iterations 7.4009500E-02 1.227349 at 110iterations 4.3934599E-02 0.6747265 at 120iterations 2.6090154E-02 0.4426541 at 130iterations 1.5476721E-02 0.2449207 at 140iterations 9.1803744E-03 0.1493454 at 150iterations 5.4569598E-03 0.1082840 at 160iterations 3.2297748E-03 5.1765442E-02 at 170iterations 1.9183701E-03 3.2897472E-02 at 180iterations finished qdiffx linear iterations at : 22:43:57 total time elapsed so far: 13.59000 # loops : 180 mean,max change (kT/e) : 1.9183701E-03 3.2897472E-02 energy calculations done at 13.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.72000 DelPhi exited at 22:43:57 13.724u 0.219s 0:14.22 97.9% 0+0k 0+0io 0pf+0w