Mon Oct 10 12:13:12 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 Mon Oct 10 2011 at 12:13:12 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7469262 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): 8.350000 56.01200 ymin,ymax (A): -8.983000 36.33300 zmin,zma (A): -3.240000 44.17400 x,y,z range (A): 47.66200 45.31600 47.41400 scale (grids/A): 0.7469262 object centre (A): 32.18100 13.67500 20.46700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 319.8998 centred at (gu) : 89.43513 90.45242 90.04491 assigned negative charge : -326.1719 centred at (gu) : 89.44498 90.54152 90.22454 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8198 nv = 96 ne = 84 npr = 43252 no. pairs analyzed = 43252 no. exposed pairs = 2715 no. arc points = 19166 no. surface atoms = 922 nbur = 1195 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 607 mr = 4587 m= 2 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.3000000 number of dielectric boundary points 4102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1527 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2087517E-08 -3.4791245E-07 midg,1,midg; midg,igrid,midg -2.1021966E-08 -2.5481827E-07 1,midg,midg; igrid,midg,midg -1.2792569E-07 -1.2578164E-07 gauss-seidel spectral radius is 0.9906608 estimated iterations to convergence 84 setup time was (sec) 0.7800000 now iterating at: 12:13:13 rms-change max change #iterations 0.2647057 36.82178 at 10iterations 3.6283709E-02 4.812775 at 20iterations 5.0094770E-03 0.6001663 at 30iterations 6.8187184E-04 8.2405090E-02 at 40iterations 9.1956063E-05 1.0589600E-02 at 50iterations finished qdiffx linear iterations at : 12:13:19 total time elapsed so far: 5.960000 # loops : 50 mean,max change (kT/e) : 9.1956063E-05 1.0589600E-02 energy calculations done at 5.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.120000 DelPhi exited at 12:13:19 6.125u 0.676s 0:07.18 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 12:13:19 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.240779 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): 8.350000 56.01200 ymin,ymax (A): -8.983000 36.33300 zmin,zma (A): -3.240000 44.17400 x,y,z range (A): 47.66200 45.31600 47.41400 scale (grids/A): 2.240779 object centre (A): 32.18100 13.67500 20.46700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 319.8998 centred at (gu) : 88.30528 91.35707 90.13470 assigned negative charge : -326.1719 centred at (gu) : 88.33485 91.62450 90.67355 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19166 grid for indexing accessible points = 1.400000 m= 35285 mr = 58920 m= 8058 mr = 27081 m= 899 mr = 5642 m= 29 mr = 491 m= 0 mr = 2 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 917 time to turn everything in is 0.8300000 number of dielectric boundary points 37575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 15773 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) : 0.7469262 object centre at (A) : 32.18100 13.67500 20.46700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5922636E-03 -0.1317516 midg,1,midg; midg,igrid,midg -3.1608488E-02 -5.1020741E-02 1,midg,midg; igrid,midg,midg -1.2968864E-03 -2.1232844E-03 gauss-seidel spectral radius is 0.9989454 estimated iterations to convergence 244 setup time was (sec) 1.450000 now iterating at: 12:13:21 rms-change max change #iterations 5.284753 232.8274 at 10iterations 2.695672 82.02776 at 20iterations 1.382897 40.68193 at 30iterations 0.7078260 19.41985 at 40iterations 0.3625620 11.53875 at 50iterations 0.1864512 5.478928 at 60iterations 9.5636256E-02 2.583150 at 70iterations 4.8898209E-02 1.320677 at 80iterations 2.5119413E-02 0.7155838 at 90iterations 1.2940049E-02 0.3696556 at 100iterations 6.6117905E-03 0.1837015 at 110iterations 3.3915511E-03 8.9650154E-02 at 120iterations finished qdiffx linear iterations at : 12:13:41 total time elapsed so far: 20.72000 # loops : 120 mean,max change (kT/e) : 3.3915511E-03 8.9650154E-02 energy calculations done at 20.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.90000 DelPhi exited at 12:13:41 20.900u 0.769s 0:21.97 98.5% 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 12:13:41 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.361168 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): 8.350000 56.01200 ymin,ymax (A): -8.983000 36.33300 zmin,zma (A): -3.240000 44.17400 x,y,z range (A): 47.66200 45.31600 47.41400 scale (grids/A): 3.361168 object centre (A): 32.18100 13.67500 20.46700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 319.8998 centred at (gu) : 87.45777 92.03551 90.20208 assigned negative charge : -326.1719 centred at (gu) : 87.50227 92.43664 91.01027 start vw surface at 0.1200000 fill in re-entrant regions at 1.030000 boundary points on vw surface= 196688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19166 grid for indexing accessible points = 1.400000 m= 106222 mr = 141766 m= 47140 mr = 88235 m= 15585 mr = 39532 m= 3765 mr = 12483 m= 503 mr = 2922 m= 17 mr = 301 m= 0 mr = 0 time to grow re-entrant surface = 1.440000 no. cavity mid-points inaccessible to solvent = 2858 time to turn everything in is 2.700000 number of dielectric boundary points 84681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.960000 number of grid points assigned charge 15824 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) : 2.240779 object centre at (A) : 32.18100 13.67500 20.46700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8350738E-02 -1.246762 midg,1,midg; midg,igrid,midg -0.2762463 -0.2569339 1,midg,midg; igrid,midg,midg -5.6453779E-02 -9.2337154E-02 gauss-seidel spectral radius is 0.9993221 estimated iterations to convergence 303 setup time was (sec) 3.330000 now iterating at: 12:13:45 rms-change max change #iterations 11.18787 316.0123 at 10iterations 6.602249 119.6489 at 20iterations 3.903809 71.08389 at 30iterations 2.301001 44.41733 at 40iterations 1.356933 23.77647 at 50iterations 0.7996327 12.85135 at 60iterations 0.4709942 7.876578 at 70iterations 0.2768885 4.727066 at 80iterations 0.1631671 2.540619 at 90iterations 9.5924623E-02 1.594053 at 100iterations 5.6318697E-02 0.8652182 at 110iterations 3.3136390E-02 0.5494013 at 120iterations 1.9517412E-02 0.2956619 at 130iterations 1.1454314E-02 0.1714897 at 140iterations 6.7556580E-03 0.1097593 at 150iterations 3.9692544E-03 6.6837311E-02 at 160iterations 2.3315875E-03 3.9500237E-02 at 170iterations 1.3723484E-03 2.2567749E-02 at 180iterations finished qdiffx linear iterations at : 12:14:17 total time elapsed so far: 34.40000 # loops : 180 mean,max change (kT/e) : 1.3723484E-03 2.2567749E-02 energy calculations done at 34.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 34.58000 DelPhi exited at 12:14:17 34.584u 0.958s 0:36.13 98.3% 0+0k 0+0io 0pf+0w