Sun Oct 9 21:10:56 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 Sun Oct 9 2011 at 21:10:56 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: SEP 142 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6432960 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): 10.34100 65.68100 ymin,ymax (A): -11.99400 38.31700 zmin,zma (A): -11.64900 41.70200 x,y,z range (A): 55.34000 50.31100 53.35100 scale (grids/A): 0.6432960 object centre (A): 38.01100 13.16150 15.02650 number of atom coordinates read : 2587 total number of charged atoms : 2441 net assigned charge : 5.525010 assigned positive charge : 391.3749 centred at (gu) : 90.57555 90.75027 90.06843 assigned negative charge : -385.8506 centred at (gu) : 90.62655 90.70103 90.04155 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7073 nv = 96 ne = 84 npr = 52178 no. pairs analyzed = 52178 no. exposed pairs = 3083 no. arc points = 22158 no. surface atoms = 1039 nbur = 1548 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 362 mr = 3868 m= 0 mr = 41 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.2100000 number of dielectric boundary points 3526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2184 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8501 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3326099E-09 1.2395923E-08 midg,1,midg; midg,igrid,midg 2.2325108E-09 1.7614196E-08 1,midg,midg; igrid,midg,midg 1.3517621E-08 2.5641940E-09 gauss-seidel spectral radius is 0.9874786 estimated iterations to convergence 73 setup time was (sec) 0.4000000 now iterating at: 21:10:57 rms-change max change #iterations 0.1509540 22.32447 at 10iterations 1.5098591E-02 2.288345 at 20iterations 1.5362991E-03 0.2112274 at 30iterations 1.5016030E-04 2.6550293E-02 at 40iterations 1.5563392E-05 2.4299622E-03 at 50iterations finished qdiffx linear iterations at : 21:11:00 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.5563392E-05 2.4299622E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 21:11:00 3.410u 0.163s 0:03.89 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 Sun Oct 9 2011 at 21:11:00 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: SEP 142 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.929888 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): 10.34100 65.68100 ymin,ymax (A): -11.99400 38.31700 zmin,zma (A): -11.64900 41.70200 x,y,z range (A): 55.34000 50.31100 53.35100 scale (grids/A): 1.929888 object centre (A): 38.01100 13.16150 15.02650 number of atom coordinates read : 2587 total number of charged atoms : 2441 net assigned charge : 5.525010 assigned positive charge : 391.3749 centred at (gu) : 91.72614 92.25043 90.20483 assigned negative charge : -385.8506 centred at (gu) : 91.87934 92.10287 90.12444 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22158 grid for indexing accessible points = 1.400000 m= 25979 mr = 52939 m= 3905 mr = 18969 m= 231 mr = 2368 m= 0 mr = 104 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2099 time to turn everything in is 0.3700000 number of dielectric boundary points 32323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19231 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) : 0.6432960 object centre at (A) : 38.01100 13.16150 15.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3507711E-02 1.4642539E-02 midg,1,midg; midg,igrid,midg -1.8622728E-02 9.7740563E-03 1,midg,midg; igrid,midg,midg -9.7374693E-03 2.2779657E-02 gauss-seidel spectral radius is 0.9986625 estimated iterations to convergence 217 setup time was (sec) 0.5800000 now iterating at: 21:11:01 rms-change max change #iterations 4.320836 159.4308 at 10iterations 2.034264 65.71024 at 20iterations 0.9613801 29.70327 at 30iterations 0.4531182 14.28053 at 40iterations 0.2137091 7.622094 at 50iterations 0.1006052 3.154190 at 60iterations 4.7486000E-02 1.461020 at 70iterations 2.2428200E-02 0.6607895 at 80iterations 1.0553200E-02 0.3245020 at 90iterations 4.9767899E-03 0.1501479 at 100iterations 2.3570112E-03 8.1071854E-02 at 110iterations 1.1099114E-03 3.3124924E-02 at 120iterations finished qdiffx linear iterations at : 21:11:08 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 1.1099114E-03 3.3124924E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 21:11:08 7.804u 0.214s 0:08.32 96.2% 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 21:11:08 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: SEP 142 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.894832 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): 10.34100 65.68100 ymin,ymax (A): -11.99400 38.31700 zmin,zma (A): -11.64900 41.70200 x,y,z range (A): 55.34000 50.31100 53.35100 scale (grids/A): 2.894832 object centre (A): 38.01100 13.16150 15.02650 number of atom coordinates read : 2587 total number of charged atoms : 2441 net assigned charge : 5.525010 assigned positive charge : 391.3749 centred at (gu) : 92.58900 93.37549 90.30719 assigned negative charge : -385.8506 centred at (gu) : 92.81889 93.15417 90.18669 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 177302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22158 grid for indexing accessible points = 1.400000 m= 86186 mr = 128240 m= 29042 mr = 70575 m= 6819 mr = 22827 m= 1083 mr = 5031 m= 80 mr = 790 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 7053 time to turn everything in is 0.9600000 number of dielectric boundary points 73007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 19527 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) : 1.929888 object centre at (A) : 38.01100 13.16150 15.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3308728 -4.4429228E-02 midg,1,midg; midg,igrid,midg -0.2940611 0.1305066 1,midg,midg; igrid,midg,midg -5.1455446E-02 0.1607409 gauss-seidel spectral radius is 0.9992654 estimated iterations to convergence 291 setup time was (sec) 1.200000 now iterating at: 21:11:10 rms-change max change #iterations 10.05543 373.5803 at 10iterations 5.845412 135.2740 at 20iterations 3.384570 65.55342 at 30iterations 1.953805 39.76639 at 40iterations 1.125098 20.15853 at 50iterations 0.6495947 13.54222 at 60iterations 0.3741719 6.683440 at 70iterations 0.2152490 3.846204 at 80iterations 0.1237488 2.268367 at 90iterations 7.1196988E-02 1.172325 at 100iterations 4.0927213E-02 0.7102498 at 110iterations 2.3532309E-02 0.4007723 at 120iterations 1.3537582E-02 0.2290897 at 130iterations 7.7793081E-03 0.1372452 at 140iterations 4.4856258E-03 7.9784870E-02 at 150iterations 2.5764017E-03 4.6256423E-02 at 160iterations 1.4836444E-03 2.6205063E-02 at 170iterations 8.5270335E-04 1.6298294E-02 at 180iterations finished qdiffx linear iterations at : 21:11:21 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 8.5270335E-04 1.6298294E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 21:11:22 12.654u 0.204s 0:13.12 97.9% 0+0k 0+0io 0pf+0w