Sun Oct 9 21:30:26 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 21:30:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3283 !!! WARNING: CYS 258 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6434820 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): -20.84100 34.48300 ymin,ymax (A): -4.386000 49.49400 zmin,zma (A): -20.04200 32.03800 x,y,z range (A): 55.32400 53.88000 52.08000 scale (grids/A): 0.6434820 object centre (A): 6.821001 22.55400 5.997999 number of atom coordinates read : 3283 total number of charged atoms : 3156 net assigned charge : 6.500021 assigned positive charge : 502.3594 centred at (gu) : 90.60184 91.04485 89.52245 assigned negative charge : -495.8610 centred at (gu) : 90.53037 91.07703 89.50565 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9282 nv = 96 ne = 84 npr = 63421 no. pairs analyzed = 63421 no. exposed pairs = 4391 no. arc points = 31771 no. surface atoms = 1449 nbur = 1834 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 537 mr = 4894 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.3900000 number of dielectric boundary points 4878 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3083 ## 301 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 11149 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4636973E-09 1.1937976E-08 midg,1,midg; midg,igrid,midg 1.2620578E-08 6.3144303E-09 1,midg,midg; igrid,midg,midg -1.1137871E-09 2.5044146E-08 gauss-seidel spectral radius is 0.9875590 estimated iterations to convergence 73 setup time was (sec) 0.6100000 now iterating at: 21:30:27 rms-change max change #iterations 0.1722320 26.25560 at 10iterations 1.6971808E-02 2.119617 at 20iterations 1.7083898E-03 0.2492847 at 30iterations 1.7617202E-04 2.3857117E-02 at 40iterations 1.9594412E-05 2.2048950E-03 at 50iterations finished qdiffx linear iterations at : 21:30:29 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.9594412E-05 2.2048950E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 21:30:30 3.414u 0.146s 0:03.91 90.7% 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 Sun Oct 9 2011 at 21:30:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3283 !!! WARNING: CYS 258 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.930446 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): -20.84100 34.48300 ymin,ymax (A): -4.386000 49.49400 zmin,zma (A): -20.04200 32.03800 x,y,z range (A): 55.32400 53.88000 52.08000 scale (grids/A): 1.930446 object centre (A): 6.821001 22.55400 5.997999 number of atom coordinates read : 3283 total number of charged atoms : 3156 net assigned charge : 6.500021 assigned positive charge : 502.3594 centred at (gu) : 91.80478 93.13364 88.56651 assigned negative charge : -495.8610 centred at (gu) : 91.59077 93.23071 88.51657 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 99662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31771 grid for indexing accessible points = 1.400000 m= 35407 mr = 67241 m= 5738 mr = 25076 m= 423 mr = 3389 m= 10 mr = 180 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 3330 time to turn everything in is 0.7200000 number of dielectric boundary points 45354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 24842 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) : 0.6434820 object centre at (A) : 6.821001 22.55400 5.997999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4357853E-03 1.2982928E-02 midg,1,midg; midg,igrid,midg 2.5278181E-02 7.5877689E-02 1,midg,midg; igrid,midg,midg 1.4850616E-02 1.7376117E-02 gauss-seidel spectral radius is 0.9987538 estimated iterations to convergence 224 setup time was (sec) 1.010000 now iterating at: 21:30:31 rms-change max change #iterations 5.033364 169.2934 at 10iterations 2.423038 70.84860 at 20iterations 1.176126 37.37964 at 30iterations 0.5652365 15.89156 at 40iterations 0.2740098 8.240318 at 50iterations 0.1319645 3.581661 at 60iterations 6.3902788E-02 1.865146 at 70iterations 3.0878704E-02 0.9340432 at 80iterations 1.4958038E-02 0.4220924 at 90iterations 7.2321007E-03 0.1972368 at 100iterations 3.5011261E-03 9.5014036E-02 at 110iterations 1.6933542E-03 5.1950932E-02 at 120iterations finished qdiffx linear iterations at : 21:30:38 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.6933542E-03 5.1950932E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 21:30:38 7.774u 0.161s 0:08.23 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 21:30:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3283 !!! WARNING: CYS 258 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.895669 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): -20.84100 34.48300 ymin,ymax (A): -4.386000 49.49400 zmin,zma (A): -20.04200 32.03800 x,y,z range (A): 55.32400 53.88000 52.08000 scale (grids/A): 2.895669 object centre (A): 6.821001 22.55400 5.997999 number of atom coordinates read : 3283 total number of charged atoms : 3156 net assigned charge : 6.500021 assigned positive charge : 502.3594 centred at (gu) : 92.70687 94.70014 87.84962 assigned negative charge : -495.8610 centred at (gu) : 92.38602 94.84595 87.77475 start vw surface at 0.1800000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 230217 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31771 grid for indexing accessible points = 1.400000 m= 114240 mr = 163552 m= 40972 mr = 91556 m= 10157 mr = 31625 m= 1707 mr = 7314 m= 143 mr = 1172 m= 5 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 11820 time to turn everything in is 1.850000 number of dielectric boundary points 102146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 25248 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) : 1.930446 object centre at (A) : 6.821001 22.55400 5.997999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1826491 0.1620155 midg,1,midg; midg,igrid,midg 0.2069459 0.7050490 1,midg,midg; igrid,midg,midg 0.3154215 0.1088911 gauss-seidel spectral radius is 0.9993192 estimated iterations to convergence 302 setup time was (sec) 2.160000 now iterating at: 21:30:40 rms-change max change #iterations 11.83308 341.2433 at 10iterations 7.182910 165.4951 at 20iterations 4.349803 102.1428 at 30iterations 2.605933 52.17178 at 40iterations 1.560908 31.00344 at 50iterations 0.9307005 15.62730 at 60iterations 0.5527290 10.59567 at 70iterations 0.3286366 5.894089 at 80iterations 0.1947123 3.365852 at 90iterations 0.1150708 1.992383 at 100iterations 6.8086095E-02 1.098656 at 110iterations 4.0249396E-02 0.7875137 at 120iterations 2.3727281E-02 0.4377899 at 130iterations 1.3983248E-02 0.2210388 at 140iterations 8.2568834E-03 0.1398599 at 150iterations 4.8667062E-03 8.3870411E-02 at 160iterations 2.8694684E-03 4.4811249E-02 at 170iterations 1.6906514E-03 2.6026487E-02 at 180iterations finished qdiffx linear iterations at : 21:30:51 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 1.6906514E-03 2.6026487E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 21:30:52 13.046u 0.183s 0:13.50 97.9% 0+0k 0+0io 0pf+0w