Sat Oct 8 12:52:16 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 Sat Oct 8 2011 at 12:52:16 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1304 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7029877 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): 0.3830000 40.44200 ymin,ymax (A): -4.387000 35.88000 zmin,zma (A): -15.78100 34.86000 x,y,z range (A): 40.05900 40.26700 50.64100 scale (grids/A): 0.7029877 object centre (A): 20.41250 15.74650 9.539500 number of atom coordinates read : 1304 total number of charged atoms : 1164 net assigned charge : 1.000011 assigned positive charge : 193.0983 centred at (gu) : 90.57944 89.05531 90.63767 assigned negative charge : -192.0980 centred at (gu) : 90.67005 88.90464 90.14768 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4445 nv = 96 ne = 84 npr = 25887 no. pairs analyzed = 25887 no. exposed pairs = 1688 no. arc points = 12458 no. surface atoms = 566 nbur = 738 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 270 mr = 2271 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1012 ## 81 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 4620 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1789304E-07 1.5459003E-07 midg,1,midg; midg,igrid,midg -4.1814740E-08 4.0213095E-08 1,midg,midg; igrid,midg,midg 2.8846292E-08 -1.9753550E-08 gauss-seidel spectral radius is 0.9893864 estimated iterations to convergence 79 setup time was (sec) 0.4600000 now iterating at: 12:52:16 rms-change max change #iterations 0.1566040 34.35457 at 10iterations 1.8093269E-02 3.023277 at 20iterations 2.2158064E-03 0.3819427 at 30iterations 2.6486017E-04 4.8843384E-02 at 40iterations 3.0978514E-05 5.8670044E-03 at 50iterations finished qdiffx linear iterations at : 12:52:20 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 3.0978514E-05 5.8670044E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 12:52:20 4.118u 0.233s 0:04.63 93.7% 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 Sat Oct 8 2011 at 12:52:20 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1304 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.108963 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): 0.3830000 40.44200 ymin,ymax (A): -4.387000 35.88000 zmin,zma (A): -15.78100 34.86000 x,y,z range (A): 40.05900 40.26700 50.64100 scale (grids/A): 2.108963 object centre (A): 20.41250 15.74650 9.539500 number of atom coordinates read : 1304 total number of charged atoms : 1164 net assigned charge : 1.000011 assigned positive charge : 193.0983 centred at (gu) : 91.73878 87.16633 91.91325 assigned negative charge : -192.0980 centred at (gu) : 92.01017 86.71385 90.44305 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 46641 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12458 grid for indexing accessible points = 1.400000 m= 16413 mr = 30526 m= 3099 mr = 11680 m= 311 mr = 2028 m= 7 mr = 180 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 22055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9243 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) : 0.7029877 object centre at (A) : 20.41250 15.74650 9.539500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7079675E-02 8.6490571E-02 midg,1,midg; midg,igrid,midg -2.6044829E-02 1.1971948E-02 1,midg,midg; igrid,midg,midg 8.5851515E-04 -2.4952204E-03 gauss-seidel spectral radius is 0.9987472 estimated iterations to convergence 224 setup time was (sec) 0.7100000 now iterating at: 12:52:21 rms-change max change #iterations 3.598930 209.9421 at 10iterations 1.717171 76.28763 at 20iterations 0.8280632 32.63283 at 30iterations 0.3998134 15.64973 at 40iterations 0.1925224 6.833601 at 50iterations 9.2801847E-02 3.684950 at 60iterations 4.4724833E-02 1.638564 at 70iterations 2.1485103E-02 0.8460541 at 80iterations 1.0378907E-02 0.3983440 at 90iterations 4.9951714E-03 0.1933842 at 100iterations 2.4169618E-03 9.6889496E-02 at 110iterations 1.1643842E-03 4.3828011E-02 at 120iterations finished qdiffx linear iterations at : 12:52:30 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 1.1643842E-03 4.3828011E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 12:52:30 9.380u 0.279s 0:09.95 96.9% 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 Sat Oct 8 2011 at 12:52:30 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1304 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.163445 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): 0.3830000 40.44200 ymin,ymax (A): -4.387000 35.88000 zmin,zma (A): -15.78100 34.86000 x,y,z range (A): 40.05900 40.26700 50.64100 scale (grids/A): 3.163445 object centre (A): 20.41250 15.74650 9.539500 number of atom coordinates read : 1304 total number of charged atoms : 1164 net assigned charge : 1.000011 assigned positive charge : 193.0983 centred at (gu) : 92.60828 85.74948 92.86985 assigned negative charge : -192.0980 centred at (gu) : 93.01530 85.07077 90.66455 start vw surface at 0.1100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 107416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12458 grid for indexing accessible points = 1.400000 m= 52458 mr = 73995 m= 19724 mr = 41913 m= 5794 mr = 15607 m= 1226 mr = 4414 m= 173 mr = 935 m= 3 mr = 120 m= 0 mr = 2 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 49808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 9312 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) : 2.108963 object centre at (A) : 20.41250 15.74650 9.539500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1160287 0.8910474 midg,1,midg; midg,igrid,midg -0.2695568 0.1212346 1,midg,midg; igrid,midg,midg -5.7354048E-03 -6.7696054E-03 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.500000 now iterating at: 12:52:32 rms-change max change #iterations 8.002566 349.3309 at 10iterations 4.572826 105.8857 at 20iterations 2.629148 59.61670 at 30iterations 1.511687 36.73880 at 40iterations 0.8662573 19.51661 at 50iterations 0.4981334 10.58824 at 60iterations 0.2860539 7.155876 at 70iterations 0.1642383 3.435886 at 80iterations 9.4255917E-02 2.315756 at 90iterations 5.4072104E-02 1.306499 at 100iterations 3.1083751E-02 0.6772079 at 110iterations 1.7848013E-02 0.3668823 at 120iterations 1.0253591E-02 0.2208960 at 130iterations 5.8946954E-03 0.1195908 at 140iterations 3.3893024E-03 7.4380875E-02 at 150iterations 1.9470196E-03 4.0908813E-02 at 160iterations 1.1197862E-03 2.6748657E-02 at 170iterations 6.4245955E-04 1.3771057E-02 at 180iterations finished qdiffx linear iterations at : 12:52:45 total time elapsed so far: 14.70000 # loops : 180 mean,max change (kT/e) : 6.4245955E-04 1.3771057E-02 energy calculations done at 14.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.88000 DelPhi exited at 12:52:46 14.881u 0.276s 0:15.43 98.1% 0+0k 0+0io 0pf+0w