Tue Oct 11 08:28:04 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 Tue Oct 11 2011 at 08:28:04 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 = 2524 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: 0.5691447 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): -2.983000 40.13700 ymin,ymax (A): -18.84500 38.17900 zmin,zma (A): -11.62700 50.92300 x,y,z range (A): 43.12000 57.02399 62.55000 scale (grids/A): 0.5691447 object centre (A): 18.57700 9.666999 19.64800 number of atom coordinates read : 2524 total number of charged atoms : 2379 net assigned charge : -1.999976 assigned positive charge : 387.7139 centred at (gu) : 89.82868 89.04823 91.40099 assigned negative charge : -389.7144 centred at (gu) : 89.77880 88.98013 91.47057 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5318 nv = 96 ne = 84 npr = 49740 no. pairs analyzed = 49740 no. exposed pairs = 3328 no. arc points = 24104 no. surface atoms = 1121 nbur = 1403 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 210 mr = 2584 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2457 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6860 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6040913E-10 -1.6917281E-09 midg,1,midg; midg,igrid,midg -1.4911570E-09 4.9829407E-10 1,midg,midg; igrid,midg,midg -9.7841857E-10 3.7428607E-10 gauss-seidel spectral radius is 0.9840392 estimated iterations to convergence 65 setup time was (sec) 0.4900000 now iterating at: 08:28:05 rms-change max change #iterations 8.3116993E-02 17.96075 at 10iterations 6.1490135E-03 1.170210 at 20iterations 4.4895272E-04 8.7991714E-02 at 30iterations 3.3563021E-05 5.7601929E-03 at 40iterations 2.4599783E-06 4.3106079E-04 at 50iterations finished qdiffx linear iterations at : 08:28:07 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 2.4599783E-06 4.3106079E-04 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 08:28:08 3.090u 0.139s 0:03.86 83.4% 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 Tue Oct 11 2011 at 08:28:08 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 = 2524 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: 1.707434 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): -2.983000 40.13700 ymin,ymax (A): -18.84500 38.17900 zmin,zma (A): -11.62700 50.92300 x,y,z range (A): 43.12000 57.02399 62.55000 scale (grids/A): 1.707434 object centre (A): 18.57700 9.666999 19.64800 number of atom coordinates read : 2524 total number of charged atoms : 2379 net assigned charge : -1.999976 assigned positive charge : 387.7139 centred at (gu) : 89.48555 87.14425 94.20229 assigned negative charge : -389.7144 centred at (gu) : 89.33616 86.94009 94.41142 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 57874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24104 grid for indexing accessible points = 1.400000 m= 17870 mr = 37138 m= 2202 mr = 12361 m= 68 mr = 1224 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1078 time to turn everything in is 0.4100000 number of dielectric boundary points 27286 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 18337 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) : 0.5691447 object centre at (A) : 18.57700 9.666999 19.64800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2045454E-02 3.2857529E-04 midg,1,midg; midg,igrid,midg -1.8881848E-02 -1.9849172E-02 1,midg,midg; igrid,midg,midg -2.5487347E-03 -7.3733565E-05 gauss-seidel spectral radius is 0.9982967 estimated iterations to convergence 192 setup time was (sec) 0.6700000 now iterating at: 08:28:09 rms-change max change #iterations 3.398367 209.1139 at 10iterations 1.451645 68.78780 at 20iterations 0.6199817 28.93681 at 30iterations 0.2641790 9.891701 at 40iterations 0.1137074 4.100345 at 50iterations 4.8518196E-02 1.912205 at 60iterations 2.0659383E-02 0.9138451 at 70iterations 8.8637043E-03 0.3280325 at 80iterations 3.7710888E-03 0.1433773 at 90iterations 1.6172727E-03 5.9386253E-02 at 100iterations 6.9232489E-04 2.5114059E-02 at 110iterations 2.9619809E-04 1.2174606E-02 at 120iterations finished qdiffx linear iterations at : 08:28:15 total time elapsed so far: 6.580000 # loops : 120 mean,max change (kT/e) : 2.9619809E-04 1.2174606E-02 energy calculations done at 6.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.750000 DelPhi exited at 08:28:16 6.755u 0.178s 0:07.54 91.7% 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 Tue Oct 11 2011 at 08:28:16 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 = 2524 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: 2.561151 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): -2.983000 40.13700 ymin,ymax (A): -18.84500 38.17900 zmin,zma (A): -11.62700 50.92300 x,y,z range (A): 43.12000 57.02399 62.55000 scale (grids/A): 2.561151 object centre (A): 18.57700 9.666999 19.64800 number of atom coordinates read : 2524 total number of charged atoms : 2379 net assigned charge : -1.999976 assigned positive charge : 387.7139 centred at (gu) : 89.22826 85.71620 96.30328 assigned negative charge : -389.7144 centred at (gu) : 89.00404 85.41005 96.61700 start vw surface at 0.1500000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 134103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24104 grid for indexing accessible points = 1.400000 m= 60298 mr = 91312 m= 18738 mr = 47080 m= 3473 mr = 14357 m= 312 mr = 2477 m= 8 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 3801 time to turn everything in is 0.9600000 number of dielectric boundary points 61524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19018 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) : 1.707434 object centre at (A) : 18.57700 9.666999 19.64800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0597317E-02 0.1398684 midg,1,midg; midg,igrid,midg -0.4948415 -0.4288785 1,midg,midg; igrid,midg,midg 4.9353001E-04 3.0571907E-03 gauss-seidel spectral radius is 0.9991632 estimated iterations to convergence 273 setup time was (sec) 1.250000 now iterating at: 08:28:17 rms-change max change #iterations 8.622937 354.3917 at 10iterations 4.857714 133.9064 at 20iterations 2.714305 71.99681 at 30iterations 1.511127 33.35399 at 40iterations 0.8424237 18.91292 at 50iterations 0.4672399 11.07631 at 60iterations 0.2594548 6.210316 at 70iterations 0.1438106 3.143005 at 80iterations 7.9615369E-02 1.680119 at 90iterations 4.4035599E-02 0.9502983 at 100iterations 2.4373995E-02 0.5162220 at 110iterations 1.3503938E-02 0.3033543 at 120iterations 7.4542584E-03 0.1442702 at 130iterations 4.1250191E-03 9.1054916E-02 at 140iterations 2.2842288E-03 4.8881054E-02 at 150iterations 1.2625635E-03 2.7793884E-02 at 160iterations 6.9951575E-04 1.4738083E-02 at 170iterations 3.8761832E-04 7.7762604E-03 at 180iterations finished qdiffx linear iterations at : 08:28:26 total time elapsed so far: 10.49000 # loops : 180 mean,max change (kT/e) : 3.8761832E-04 7.7762604E-03 energy calculations done at 10.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.66000 DelPhi exited at 08:28:27 10.660u 0.170s 0:11.12 97.3% 0+0k 0+0io 0pf+0w