Sun Oct 9 19:26:38 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 Sun Oct 9 2011 at 19:26:38 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4940 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5645238 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): 3.219000 63.74600 ymin,ymax (A): -9.061000 52.93600 zmin,zma (A): -1.841000 61.22100 x,y,z range (A): 60.52700 61.99700 63.06200 scale (grids/A): 0.5645238 object centre (A): 33.48250 21.93750 29.69000 number of atom coordinates read : 4940 total number of charged atoms : 4798 net assigned charge : -1.259951 assigned positive charge : 756.5193 centred at (gu) : 88.23135 89.24618 89.12640 assigned negative charge : -757.7845 centred at (gu) : 88.09484 89.25155 89.11345 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 10208 nv = 96 ne = 84 npr = 101326 no. pairs analyzed = 101326 no. exposed pairs = 5677 no. arc points = 38570 no. surface atoms = 1942 nbur = 2998 mkacc time = 0.2200000 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 = 1.540000 m= 500 mr = 5904 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4003 ## 451 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 13482 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6889775E-10 1.5264273E-10 midg,1,midg; midg,igrid,midg 3.0471708E-11 -1.7823570E-10 1,midg,midg; igrid,midg,midg -4.8756243E-09 1.8656570E-09 gauss-seidel spectral radius is 0.9839541 estimated iterations to convergence 65 setup time was (sec) 0.7000000 now iterating at: 19:26:39 rms-change max change #iterations 0.1210356 16.83685 at 10iterations 1.3071639E-02 1.803947 at 20iterations 4.0739654E-03 0.6170349 at 30iterations 1.7110648E-03 0.2623253 at 40iterations 7.3583459E-04 0.1109276 at 50iterations finished qdiffx linear iterations at : 19:26:42 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 7.3583459E-04 0.1109276 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 19:26:42 3.633u 0.241s 0:04.29 90.2% 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 19:26:42 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4940 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.693571 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): 3.219000 63.74600 ymin,ymax (A): -9.061000 52.93600 zmin,zma (A): -1.841000 61.22100 x,y,z range (A): 60.52700 61.99700 63.06200 scale (grids/A): 1.693571 object centre (A): 33.48250 21.93750 29.69000 number of atom coordinates read : 4940 total number of charged atoms : 4798 net assigned charge : -1.259951 assigned positive charge : 756.5193 centred at (gu) : 84.69264 87.73710 87.37805 assigned negative charge : -757.7845 centred at (gu) : 84.28429 87.75435 87.34032 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 114496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38570 grid for indexing accessible points = 1.400000 m= 38237 mr = 83618 m= 4616 mr = 27481 m= 185 mr = 2399 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 43997 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 361 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 37069 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) : 0.5645238 object centre at (A) : 33.48250 21.93750 29.69000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0354947E-02 -2.7179740E-02 midg,1,midg; midg,igrid,midg 6.9751637E-03 9.0755736E-03 1,midg,midg; igrid,midg,midg -2.2092147E-02 3.8625356E-02 gauss-seidel spectral radius is 0.9984903 estimated iterations to convergence 204 setup time was (sec) 1.050000 now iterating at: 19:26:44 rms-change max change #iterations 4.938840 194.8118 at 10iterations 2.225178 62.38773 at 20iterations 1.004412 31.61649 at 30iterations 0.4546331 14.74658 at 40iterations 0.2060015 5.728943 at 50iterations 9.4220921E-02 2.809662 at 60iterations 4.3937072E-02 1.275620 at 70iterations 2.1378642E-02 0.6233749 at 80iterations 1.1377952E-02 0.4051743 at 90iterations 6.7949602E-03 0.2233009 at 100iterations 4.5258556E-03 0.1463995 at 110iterations 3.2216690E-03 0.1036148 at 120iterations finished qdiffx linear iterations at : 19:26:51 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 3.2216690E-03 0.1036148 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 19:26:51 8.245u 0.305s 0:08.88 96.1% 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 19:26:51 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4940 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.540357 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): 3.219000 63.74600 ymin,ymax (A): -9.061000 52.93600 zmin,zma (A): -1.841000 61.22100 x,y,z range (A): 60.52700 61.99700 63.06200 scale (grids/A): 2.540357 object centre (A): 33.48250 21.93750 29.69000 number of atom coordinates read : 4940 total number of charged atoms : 4798 net assigned charge : -1.259951 assigned positive charge : 756.5193 centred at (gu) : 82.03861 86.60534 86.06673 assigned negative charge : -757.7845 centred at (gu) : 81.42641 86.63145 86.01055 start vw surface at 0.1900000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 266764 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38570 grid for indexing accessible points = 1.400000 m= 130813 mr = 203639 m= 40053 mr = 106596 m= 7542 mr = 30894 m= 777 mr = 5130 m= 31 mr = 433 m= 0 mr = 6 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.920000 number of dielectric boundary points 99282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 38350 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) : 1.693571 object centre at (A) : 33.48250 21.93750 29.69000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5286592 -0.6778218 midg,1,midg; midg,igrid,midg -2.6562454E-02 2.3246843E-02 1,midg,midg; igrid,midg,midg -0.4055983 0.6144045 gauss-seidel spectral radius is 0.9992636 estimated iterations to convergence 291 setup time was (sec) 2.260000 now iterating at: 19:26:54 rms-change max change #iterations 12.33692 351.1054 at 10iterations 7.292561 153.4531 at 20iterations 4.280907 79.54477 at 30iterations 2.504896 43.56561 at 40iterations 1.458063 27.98742 at 50iterations 0.8476342 13.89180 at 60iterations 0.4914898 8.251974 at 70iterations 0.2842853 4.367950 at 80iterations 0.1651530 2.645618 at 90iterations 9.5952123E-02 1.580654 at 100iterations 5.5894278E-02 0.9130936 at 110iterations 3.2899197E-02 0.5458374 at 120iterations 1.9733885E-02 0.3326111 at 130iterations 1.2265764E-02 0.2153969 at 140iterations 8.0002584E-03 0.1501007 at 150iterations 5.5708331E-03 0.1101227 at 160iterations 4.1440334E-03 8.4487915E-02 at 170iterations 3.2371879E-03 6.2805176E-02 at 180iterations finished qdiffx linear iterations at : 19:27:07 total time elapsed so far: 15.72000 # loops : 180 mean,max change (kT/e) : 3.2371879E-03 6.2805176E-02 energy calculations done at 15.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.90000 DelPhi exited at 19:27:08 15.901u 0.310s 0:16.57 97.8% 0+0k 0+0io 0pf+0w