Tue Oct 11 08:29:40 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 Tue Oct 11 2011 at 08:29:40 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: 390 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIR 85 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: GLU 295 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6396320 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): -4.861000 50.79600 ymin,ymax (A): 9.492001 61.91700 zmin,zma (A): 0.5830001 55.13800 x,y,z range (A): 55.65700 52.42500 54.55500 scale (grids/A): 0.6396320 object centre (A): 22.96750 35.70450 27.86050 number of atom coordinates read : 2859 total number of charged atoms : 2627 net assigned charge : 4.039016 assigned positive charge : 424.6488 centred at (gu) : 89.51469 90.28001 91.20961 assigned negative charge : -420.6102 centred at (gu) : 89.68754 90.18956 91.13486 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7471 nv = 96 ne = 84 npr = 59785 no. pairs analyzed = 59785 no. exposed pairs = 3391 no. arc points = 23973 no. surface atoms = 1157 nbur = 1702 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4116 m= 0 mr = 71 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3700000 number of dielectric boundary points 3733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2273 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8971 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9078140E-09 1.9241980E-08 midg,1,midg; midg,igrid,midg -5.4975544E-09 1.7796024E-08 1,midg,midg; igrid,midg,midg 2.9732217E-08 -1.4783155E-08 gauss-seidel spectral radius is 0.9873543 estimated iterations to convergence 73 setup time was (sec) 0.6600000 now iterating at: 08:29:41 rms-change max change #iterations 0.1566275 23.28250 at 10iterations 1.5950188E-02 2.209805 at 20iterations 1.6834608E-03 0.2601852 at 30iterations 2.2192193E-04 3.4648895E-02 at 40iterations 5.2687265E-05 8.8462830E-03 at 50iterations finished qdiffx linear iterations at : 08:29:44 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 5.2687265E-05 8.8462830E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 08:29:45 4.234u 0.256s 0:05.06 88.5% 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 Tue Oct 11 2011 at 08:29:45 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: 390 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIR 85 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: GLU 295 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.918896 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): -4.861000 50.79600 ymin,ymax (A): 9.492001 61.91700 zmin,zma (A): 0.5830001 55.13800 x,y,z range (A): 55.65700 52.42500 54.55500 scale (grids/A): 1.918896 object centre (A): 22.96750 35.70450 27.86050 number of atom coordinates read : 2859 total number of charged atoms : 2627 net assigned charge : 4.039016 assigned positive charge : 424.6488 centred at (gu) : 88.54344 90.83916 93.62803 assigned negative charge : -420.6102 centred at (gu) : 89.06216 90.56852 93.40417 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 79760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23973 grid for indexing accessible points = 1.400000 m= 30399 mr = 54936 m= 5497 mr = 22796 m= 373 mr = 3632 m= 5 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 2037 time to turn everything in is 0.7200000 number of dielectric boundary points 34520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20673 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) : 0.6396320 object centre at (A) : 22.96750 35.70450 27.86050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0381393E-02 9.7566970E-02 midg,1,midg; midg,igrid,midg -6.5403697E-03 -2.7679892E-03 1,midg,midg; igrid,midg,midg 6.3701533E-02 -5.9676189E-02 gauss-seidel spectral radius is 0.9986763 estimated iterations to convergence 218 setup time was (sec) 1.040000 now iterating at: 08:29:46 rms-change max change #iterations 4.550055 190.8615 at 10iterations 2.151757 89.75994 at 20iterations 1.022432 29.99870 at 30iterations 0.4862087 17.24988 at 40iterations 0.2300220 6.627255 at 50iterations 0.1092952 3.100066 at 60iterations 5.1717494E-02 1.631531 at 70iterations 2.4697227E-02 0.7366219 at 80iterations 1.1725627E-02 0.3473897 at 90iterations 5.5786525E-03 0.1927614 at 100iterations 2.6852766E-03 8.7711334E-02 at 110iterations 1.3000914E-03 4.0731430E-02 at 120iterations finished qdiffx linear iterations at : 08:29:55 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 1.3000914E-03 4.0731430E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.680000 DelPhi exited at 08:29:56 9.685u 0.247s 0:10.68 92.8% 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 08:29:56 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: 390 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIR 85 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: GLU 295 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.878344 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): -4.861000 50.79600 ymin,ymax (A): 9.492001 61.91700 zmin,zma (A): 0.5830001 55.13800 x,y,z range (A): 55.65700 52.42500 54.55500 scale (grids/A): 2.878344 object centre (A): 22.96750 35.70450 27.86050 number of atom coordinates read : 2859 total number of charged atoms : 2627 net assigned charge : 4.039016 assigned positive charge : 424.6488 centred at (gu) : 87.81500 91.25885 95.44208 assigned negative charge : -420.6102 centred at (gu) : 88.59316 90.85275 95.10617 start vw surface at 0.1900000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 183920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23973 grid for indexing accessible points = 1.400000 m= 95429 mr = 132823 m= 37835 mr = 78370 m= 10092 mr = 30857 m= 1632 mr = 7920 m= 104 mr = 1145 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 6663 time to turn everything in is 1.740000 number of dielectric boundary points 77845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 21015 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) : 1.918896 object centre at (A) : 22.96750 35.70450 27.86050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2212777 1.390601 midg,1,midg; midg,igrid,midg -2.2211403E-02 -0.1850229 1,midg,midg; igrid,midg,midg 1.109813 -0.7817901 gauss-seidel spectral radius is 0.9992710 estimated iterations to convergence 292 setup time was (sec) 2.070000 now iterating at: 08:29:58 rms-change max change #iterations 10.51124 347.8073 at 10iterations 6.169388 146.0049 at 20iterations 3.602630 84.67905 at 30iterations 2.096092 54.26043 at 40iterations 1.220744 28.49055 at 50iterations 0.7090845 13.72351 at 60iterations 0.4108795 8.623066 at 70iterations 0.2387779 4.601181 at 80iterations 0.1379524 2.807346 at 90iterations 7.9828575E-02 1.677757 at 100iterations 4.6421945E-02 0.8536530 at 110iterations 2.6802547E-02 0.4627209 at 120iterations 1.5488018E-02 0.2838418 at 130iterations 8.9631155E-03 0.1533313 at 140iterations 5.2004196E-03 9.4175339E-02 at 150iterations 3.0189285E-03 5.3302765E-02 at 160iterations 1.7589234E-03 2.9964447E-02 at 170iterations 1.0321483E-03 2.0159721E-02 at 180iterations finished qdiffx linear iterations at : 08:30:11 total time elapsed so far: 15.57000 # loops : 180 mean,max change (kT/e) : 1.0321483E-03 2.0159721E-02 energy calculations done at 15.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.75000 DelPhi exited at 08:30:13 15.750u 0.284s 0:16.84 95.1% 0+0k 0+0io 0pf+0w