Mon Oct 10 14:01:29 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 Mon Oct 10 2011 at 14:01:29 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1670 !!! WARNING: GLM 89 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7615625 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): -38.49700 8.249001 ymin,ymax (A): 2.552000 49.18800 zmin,zma (A): 31.42400 73.43800 x,y,z range (A): 46.74600 46.63600 42.01400 scale (grids/A): 0.7615625 object centre (A): -15.12400 25.87000 52.43100 number of atom coordinates read : 1670 total number of charged atoms : 1528 net assigned charge : 5.406009 assigned positive charge : 244.6254 centred at (gu) : 89.98685 90.03108 89.93501 assigned negative charge : -239.2193 centred at (gu) : 90.00307 89.92516 90.02705 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6923 nv = 96 ne = 84 npr = 31944 no. pairs analyzed = 31944 no. exposed pairs = 2384 no. arc points = 16874 no. surface atoms = 797 nbur = 873 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 582 mr = 3642 m= 7 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.2800000 number of dielectric boundary points 3769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1137 ## 79 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6769 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5946201E-07 4.1621682E-08 midg,1,midg; midg,igrid,midg 2.5431548E-08 2.7386190E-07 1,midg,midg; igrid,midg,midg 1.6941010E-07 1.3092773E-07 gauss-seidel spectral radius is 0.9909765 estimated iterations to convergence 85 setup time was (sec) 0.5300000 now iterating at: 14:01:30 rms-change max change #iterations 0.2392313 36.16277 at 10iterations 3.3592317E-02 4.967499 at 20iterations 4.8427875E-03 0.6632004 at 30iterations 6.8990188E-04 0.1009078 at 40iterations 1.0767237E-04 1.4402390E-02 at 50iterations finished qdiffx linear iterations at : 14:01:33 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.0767237E-04 1.4402390E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 14:01:34 3.589u 0.192s 0:04.93 76.4% 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 Mon Oct 10 2011 at 14:01:34 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1670 !!! WARNING: GLM 89 has a net charge of -0.0940 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: 2.284688 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): -38.49700 8.249001 ymin,ymax (A): 2.552000 49.18800 zmin,zma (A): 31.42400 73.43800 x,y,z range (A): 46.74600 46.63600 42.01400 scale (grids/A): 2.284688 object centre (A): -15.12400 25.87000 52.43100 number of atom coordinates read : 1670 total number of charged atoms : 1528 net assigned charge : 5.406009 assigned positive charge : 244.6254 centred at (gu) : 89.96072 90.09349 89.80540 assigned negative charge : -239.2193 centred at (gu) : 90.00954 89.77558 90.08119 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 72136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16874 grid for indexing accessible points = 1.400000 m= 29380 mr = 48022 m= 7507 mr = 21707 m= 976 mr = 5248 m= 42 mr = 535 m= 0 mr = 10 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1042 time to turn everything in is 0.6400000 number of dielectric boundary points 34519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 12187 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) : 0.7615625 object centre at (A) : -15.12400 25.87000 52.43100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8621923E-02 -3.1536724E-02 midg,1,midg; midg,igrid,midg 2.0888615E-02 0.1203358 1,midg,midg; igrid,midg,midg 2.5506645E-02 -1.1750227E-02 gauss-seidel spectral radius is 0.9989541 estimated iterations to convergence 245 setup time was (sec) 0.9500000 now iterating at: 14:01:36 rms-change max change #iterations 4.609619 187.9342 at 10iterations 2.369765 80.46431 at 20iterations 1.213484 39.34838 at 30iterations 0.6259985 19.24261 at 40iterations 0.3215123 9.647072 at 50iterations 0.1652125 5.404626 at 60iterations 8.5270159E-02 2.535839 at 70iterations 4.3917261E-02 1.278618 at 80iterations 2.2648104E-02 0.7230591 at 90iterations 1.1653553E-02 0.3559251 at 100iterations 6.0209078E-03 0.1842957 at 110iterations 3.0996485E-03 9.9464417E-02 at 120iterations finished qdiffx linear iterations at : 14:01:43 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 3.0996485E-03 9.9464417E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.320000 DelPhi exited at 14:01:44 8.321u 0.227s 0:09.39 90.9% 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 Mon Oct 10 2011 at 14:01:44 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1670 !!! WARNING: GLM 89 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.427031 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): -38.49700 8.249001 ymin,ymax (A): 2.552000 49.18800 zmin,zma (A): 31.42400 73.43800 x,y,z range (A): 46.74600 46.63600 42.01400 scale (grids/A): 3.427031 object centre (A): -15.12400 25.87000 52.43100 number of atom coordinates read : 1670 total number of charged atoms : 1528 net assigned charge : 5.406009 assigned positive charge : 244.6254 centred at (gu) : 89.94103 90.14027 89.70818 assigned negative charge : -239.2193 centred at (gu) : 90.01434 89.66341 90.12175 start vw surface at 0.1400000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 166160 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16874 grid for indexing accessible points = 1.400000 m= 87489 mr = 116397 m= 40048 mr = 70916 m= 14670 mr = 32681 m= 3747 mr = 11666 m= 580 mr = 2819 m= 33 mr = 386 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 3436 time to turn everything in is 2.050000 number of dielectric boundary points 77852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 12224 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) : 2.284688 object centre at (A) : -15.12400 25.87000 52.43100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1678005 -0.3656720 midg,1,midg; midg,igrid,midg 0.1434045 1.461144 1,midg,midg; igrid,midg,midg 0.4564566 -0.5139413 gauss-seidel spectral radius is 0.9993317 estimated iterations to convergence 305 setup time was (sec) 2.410000 now iterating at: 14:01:47 rms-change max change #iterations 10.02871 309.8328 at 10iterations 6.065414 148.4133 at 20iterations 3.659128 84.22266 at 30iterations 2.193337 38.95973 at 40iterations 1.312502 24.59734 at 50iterations 0.7835053 14.90720 at 60iterations 0.4675617 8.237192 at 70iterations 0.2779576 4.989087 at 80iterations 0.1654683 2.890770 at 90iterations 9.8300338E-02 1.696292 at 100iterations 5.8501624E-02 1.065342 at 110iterations 3.4718841E-02 0.6025276 at 120iterations 2.0545147E-02 0.3543320 at 130iterations 1.2200431E-02 0.2294512 at 140iterations 7.2549339E-03 0.1498932 at 150iterations 4.3103751E-03 8.3114624E-02 at 160iterations 2.5758690E-03 4.4836044E-02 at 170iterations 1.5531617E-03 2.8131247E-02 at 180iterations finished qdiffx linear iterations at : 14:01:57 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 1.5531617E-03 2.8131247E-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) 13.07000 DelPhi exited at 14:01:58 13.069u 0.263s 0:14.06 94.7% 0+0k 0+0io 0pf+0w