Sat Oct 15 12:26:12 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 15 2011 at 12:26:12 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6653459 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): 1.259000 44.13000 ymin,ymax (A): -9.286000 37.76000 zmin,zma (A): -24.70100 28.80500 x,y,z range (A): 42.87100 47.04600 53.50600 scale (grids/A): 0.6653459 object centre (A): 22.69450 14.23700 2.052000 number of atom coordinates read : 1946 total number of charged atoms : 1803 net assigned charge : 0.4060155 assigned positive charge : 289.9430 centred at (gu) : 90.06409 89.29187 88.27438 assigned negative charge : -289.5371 centred at (gu) : 89.87749 89.14487 88.17744 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5747 nv = 96 ne = 84 npr = 40435 no. pairs analyzed = 40435 no. exposed pairs = 2452 no. arc points = 17675 no. surface atoms = 825 nbur = 1121 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3086 m= 2 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.1600000 number of dielectric boundary points 2982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1724 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6676 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1351553E-08 1.2504938E-08 midg,1,midg; midg,igrid,midg -2.7203345E-08 2.2517634E-08 1,midg,midg; igrid,midg,midg -2.9901436E-08 3.2994400E-08 gauss-seidel spectral radius is 0.9882318 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 12:26:13 rms-change max change #iterations 0.1476148 27.22671 at 10iterations 1.5580053E-02 2.252991 at 20iterations 1.6609385E-03 0.2818699 at 30iterations 1.8206355E-04 3.0437469E-02 at 40iterations 1.9476996E-05 3.4103394E-03 at 50iterations finished qdiffx linear iterations at : 12:26:16 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 1.9476996E-05 3.4103394E-03 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.880000 DelPhi exited at 12:26:17 3.884u 0.247s 0:04.41 93.4% 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 Sat Oct 15 2011 at 12:26:17 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.996038 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): 1.259000 44.13000 ymin,ymax (A): -9.286000 37.76000 zmin,zma (A): -24.70100 28.80500 x,y,z range (A): 42.87100 47.04600 53.50600 scale (grids/A): 1.996038 object centre (A): 22.69450 14.23700 2.052000 number of atom coordinates read : 1946 total number of charged atoms : 1803 net assigned charge : 0.4060155 assigned positive charge : 289.9430 centred at (gu) : 90.19219 87.87568 84.82301 assigned negative charge : -289.5371 centred at (gu) : 89.63267 87.43465 84.53230 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 60939 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17675 grid for indexing accessible points = 1.400000 m= 22799 mr = 41050 m= 4010 mr = 16919 m= 258 mr = 2623 m= 2 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 722 time to turn everything in is 0.3400000 number of dielectric boundary points 27326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 14234 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) : 0.6653459 object centre at (A) : 22.69450 14.23700 2.052000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1137220E-02 3.2415465E-02 midg,1,midg; midg,igrid,midg -2.0348148E-02 1.2986012E-02 1,midg,midg; igrid,midg,midg -2.6159653E-02 2.6763460E-02 gauss-seidel spectral radius is 0.9986871 estimated iterations to convergence 219 setup time was (sec) 0.6000000 now iterating at: 12:26:18 rms-change max change #iterations 3.992094 223.1115 at 10iterations 1.885622 71.18862 at 20iterations 0.8927317 33.05258 at 30iterations 0.4237923 14.84324 at 40iterations 0.2007148 6.614399 at 50iterations 9.5501296E-02 3.621565 at 60iterations 4.5332637E-02 1.552059 at 70iterations 2.1453060E-02 0.6992645 at 80iterations 1.0202180E-02 0.3549843 at 90iterations 4.8376191E-03 0.1857033 at 100iterations 2.2993821E-03 9.8249435E-02 at 110iterations 1.0918548E-03 3.6174774E-02 at 120iterations finished qdiffx linear iterations at : 12:26:26 total time elapsed so far: 8.870000 # loops : 120 mean,max change (kT/e) : 1.0918548E-03 3.6174774E-02 energy calculations done at 8.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.000000 DelPhi exited at 12:26:26 9.002u 0.284s 0:09.59 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 15 2011 at 12:26:27 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.994057 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): 1.259000 44.13000 ymin,ymax (A): -9.286000 37.76000 zmin,zma (A): -24.70100 28.80500 x,y,z range (A): 42.87100 47.04600 53.50600 scale (grids/A): 2.994057 object centre (A): 22.69450 14.23700 2.052000 number of atom coordinates read : 1946 total number of charged atoms : 1803 net assigned charge : 0.4060155 assigned positive charge : 289.9430 centred at (gu) : 90.28841 86.81357 82.23460 assigned negative charge : -289.5371 centred at (gu) : 89.44892 86.15198 81.79847 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 140339 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17675 grid for indexing accessible points = 1.400000 m= 71437 mr = 99125 m= 27908 mr = 58381 m= 7366 mr = 22786 m= 1132 mr = 5672 m= 67 mr = 756 m= 4 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2632 time to turn everything in is 0.8600000 number of dielectric boundary points 61498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 14424 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) : 1.996038 object centre at (A) : 22.69450 14.23700 2.052000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6009567 0.9728059 midg,1,midg; midg,igrid,midg -0.1208876 0.1399250 1,midg,midg; igrid,midg,midg -0.2267640 0.2591457 gauss-seidel spectral radius is 0.9992596 estimated iterations to convergence 290 setup time was (sec) 1.140000 now iterating at: 12:26:28 rms-change max change #iterations 9.163067 401.1165 at 10iterations 5.287422 152.4403 at 20iterations 3.049526 74.28012 at 30iterations 1.753766 38.13747 at 40iterations 1.010072 19.24158 at 50iterations 0.5798787 11.80916 at 60iterations 0.3340738 6.999227 at 70iterations 0.1916147 4.005096 at 80iterations 0.1098141 2.281372 at 90iterations 6.2946439E-02 1.209396 at 100iterations 3.6179610E-02 0.6699734 at 110iterations 2.0714188E-02 0.4240322 at 120iterations 1.1893432E-02 0.2433987 at 130iterations 6.8071843E-03 0.1359587 at 140iterations 3.9076568E-03 7.4504852E-02 at 150iterations 2.2446830E-03 4.4153452E-02 at 160iterations 1.2890913E-03 2.7009010E-02 at 170iterations 7.3730882E-04 1.4268875E-02 at 180iterations finished qdiffx linear iterations at : 12:26:42 total time elapsed so far: 14.36000 # loops : 180 mean,max change (kT/e) : 7.3730882E-04 1.4268875E-02 energy calculations done at 14.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.50000 DelPhi exited at 12:26:42 14.503u 0.290s 0:15.51 95.3% 0+0k 0+0io 0pf+0w