Mon Oct 10 10:30:00 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 Mon Oct 10 2011 at 10:30:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2533 !!! WARNING: MN9 955 has a net charge of 1.4000 !!! WARNING: MN9 956 has a net charge of 1.4000 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: 0.6111168 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): -30.93600 27.31800 ymin,ymax (A): 41.35500 98.21600 zmin,zma (A): 3.006000 52.69200 x,y,z range (A): 58.25400 56.86100 49.68600 scale (grids/A): 0.6111168 object centre (A): -1.809000 69.78550 27.84900 number of atom coordinates read : 2533 total number of charged atoms : 2390 net assigned charge : 10.30002 assigned positive charge : 385.2361 centred at (gu) : 87.74762 89.71592 87.56524 assigned negative charge : -374.9368 centred at (gu) : 87.60982 89.61378 87.54081 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6568 nv = 96 ne = 84 npr = 48012 no. pairs analyzed = 48012 no. exposed pairs = 3604 no. arc points = 26025 no. surface atoms = 1191 nbur = 1342 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 3171 m= 0 mr = 20 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2586 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7942 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8920320E-09 4.5243760E-09 midg,1,midg; midg,igrid,midg 1.4791333E-09 1.0673285E-08 1,midg,midg; igrid,midg,midg -9.2329139E-10 7.9773237E-09 gauss-seidel spectral radius is 0.9861447 estimated iterations to convergence 70 setup time was (sec) 0.5800000 now iterating at: 10:30:01 rms-change max change #iterations 0.1153443 15.73064 at 10iterations 1.0305679E-02 1.364391 at 20iterations 1.0007522E-03 0.1441936 at 30iterations 1.4231754E-04 2.4459839E-02 at 40iterations 3.1226275E-05 5.6343079E-03 at 50iterations finished qdiffx linear iterations at : 10:30:04 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 3.1226275E-05 5.6343079E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 10:30:05 4.436u 0.407s 0:05.11 94.5% 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 Mon Oct 10 2011 at 10:30:05 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 = 2533 !!! WARNING: MN9 955 has a net charge of 1.4000 !!! WARNING: MN9 956 has a net charge of 1.4000 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: 1.833351 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): -30.93600 27.31800 ymin,ymax (A): 41.35500 98.21600 zmin,zma (A): 3.006000 52.69200 x,y,z range (A): 58.25400 56.86100 49.68600 scale (grids/A): 1.833351 object centre (A): -1.809000 69.78550 27.84900 number of atom coordinates read : 2533 total number of charged atoms : 2390 net assigned charge : 10.30002 assigned positive charge : 385.2361 centred at (gu) : 83.24253 89.14742 82.69531 assigned negative charge : -374.9368 centred at (gu) : 82.82920 88.84120 82.62239 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26025 grid for indexing accessible points = 1.400000 m= 24020 mr = 45785 m= 3449 mr = 16278 m= 192 mr = 1783 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 34269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 18725 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) : 0.6111168 object centre at (A) : -1.809000 69.78550 27.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1679314E-02 4.6668616E-03 midg,1,midg; midg,igrid,midg 7.0425114E-03 2.6232317E-02 1,midg,midg; igrid,midg,midg 2.0174460E-02 1.2772374E-02 gauss-seidel spectral radius is 0.9985383 estimated iterations to convergence 207 setup time was (sec) 0.9600000 now iterating at: 10:30:06 rms-change max change #iterations 3.908817 187.9309 at 10iterations 1.776667 59.91914 at 20iterations 0.8068341 27.34602 at 30iterations 0.3669623 11.66819 at 40iterations 0.1668745 6.214911 at 50iterations 7.5683296E-02 2.978073 at 60iterations 3.4565426E-02 1.158192 at 70iterations 1.5801094E-02 0.4936333 at 80iterations 7.1780137E-03 0.2482491 at 90iterations 3.2938377E-03 0.1157608 at 100iterations 1.5059336E-03 4.9986839E-02 at 110iterations 6.9668418E-04 2.3934841E-02 at 120iterations finished qdiffx linear iterations at : 10:30:16 total time elapsed so far: 10.40000 # loops : 120 mean,max change (kT/e) : 6.9668418E-04 2.3934841E-02 energy calculations done at 10.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.57000 DelPhi exited at 10:30:16 10.579u 0.450s 0:11.30 97.5% 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 Mon Oct 10 2011 at 10:30:16 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 = 2533 !!! WARNING: MN9 955 has a net charge of 1.4000 !!! WARNING: MN9 956 has a net charge of 1.4000 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: 2.750026 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): -30.93600 27.31800 ymin,ymax (A): 41.35500 98.21600 zmin,zma (A): 3.006000 52.69200 x,y,z range (A): 58.25400 56.86100 49.68600 scale (grids/A): 2.750026 object centre (A): -1.809000 69.78550 27.84900 number of atom coordinates read : 2533 total number of charged atoms : 2390 net assigned charge : 10.30002 assigned positive charge : 385.2361 centred at (gu) : 79.86372 88.72105 79.04300 assigned negative charge : -374.9368 centred at (gu) : 79.24377 88.26174 78.93359 start vw surface at 0.1100000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 162919 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26025 grid for indexing accessible points = 1.400000 m= 78060 mr = 112182 m= 26991 mr = 60334 m= 5709 mr = 20267 m= 690 mr = 3849 m= 36 mr = 378 m= 0 mr = 10 time to grow re-entrant surface = 0.9200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 77385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 19117 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) : 1.833351 object centre at (A) : -1.809000 69.78550 27.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3813039 -2.8707225E-02 midg,1,midg; midg,igrid,midg 0.1128599 0.4483212 1,midg,midg; igrid,midg,midg 0.3252002 7.2121131E-03 gauss-seidel spectral radius is 0.9992544 estimated iterations to convergence 289 setup time was (sec) 1.830000 now iterating at: 10:30:18 rms-change max change #iterations 9.717319 307.5977 at 10iterations 5.804800 144.7471 at 20iterations 3.405383 83.33408 at 30iterations 1.992480 40.79444 at 40iterations 1.160331 25.70962 at 50iterations 0.6738918 14.32547 at 60iterations 0.3889595 8.650135 at 70iterations 0.2250357 4.927069 at 80iterations 0.1298227 2.561868 at 90iterations 7.4785285E-02 1.562031 at 100iterations 4.3012694E-02 0.7859201 at 110iterations 2.4718545E-02 0.5354767 at 120iterations 1.4217135E-02 0.2772064 at 130iterations 8.1647402E-03 0.1717739 at 140iterations 4.6998253E-03 8.4253073E-02 at 150iterations 2.7059703E-03 5.0455093E-02 at 160iterations 1.5672337E-03 3.7687302E-02 at 170iterations 9.1089291E-04 1.8301010E-02 at 180iterations finished qdiffx linear iterations at : 10:30:36 total time elapsed so far: 19.11000 # loops : 180 mean,max change (kT/e) : 9.1089291E-04 1.8301010E-02 energy calculations done at 19.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.28000 DelPhi exited at 10:30:36 19.284u 0.486s 0:20.04 98.6% 0+0k 0+0io 0pf+0w