Tue Oct 11 03:57:08 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 Tue Oct 11 2011 at 03:57:08 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 0.6606295 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): -9.723000 36.64300 ymin,ymax (A): -27.67400 21.62000 zmin,zma (A): -8.275000 45.61300 x,y,z range (A): 46.36600 49.29400 53.88800 scale (grids/A): 0.6606295 object centre (A): 13.46000 -3.027000 18.66900 number of atom coordinates read : 2700 total number of charged atoms : 2598 net assigned charge : 3.926016 assigned positive charge : 420.2567 centred at (gu) : 89.42810 90.82133 91.47253 assigned negative charge : -416.3312 centred at (gu) : 89.17482 90.67675 91.50414 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8102 nv = 96 ne = 84 npr = 52250 no. pairs analyzed = 52250 no. exposed pairs = 3442 no. arc points = 24058 no. surface atoms = 1150 nbur = 1550 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 480 mr = 4582 m= 1 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3000000 number of dielectric boundary points 3932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2321 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9554 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2725752E-08 4.6660387E-09 midg,1,midg; midg,igrid,midg -1.7707730E-08 4.8736041E-08 1,midg,midg; igrid,midg,midg -5.1531586E-08 5.6257697E-08 gauss-seidel spectral radius is 0.9881350 estimated iterations to convergence 75 setup time was (sec) 0.5500000 now iterating at: 03:57:09 rms-change max change #iterations 0.1776819 23.26984 at 10iterations 1.8884722E-02 3.550744 at 20iterations 2.0436954E-03 0.2787666 at 30iterations 2.2844497E-04 3.0162811E-02 at 40iterations 2.7934038E-05 3.9882660E-03 at 50iterations finished qdiffx linear iterations at : 03:57:12 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 2.7934038E-05 3.9882660E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 03:57:13 3.892u 0.375s 0:05.01 85.0% 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 Tue Oct 11 2011 at 03:57:13 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 1.981888 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): -9.723000 36.64300 ymin,ymax (A): -27.67400 21.62000 zmin,zma (A): -8.275000 45.61300 x,y,z range (A): 46.36600 49.29400 53.88800 scale (grids/A): 1.981888 object centre (A): 13.46000 -3.027000 18.66900 number of atom coordinates read : 2700 total number of charged atoms : 2598 net assigned charge : 3.926016 assigned positive charge : 420.2567 centred at (gu) : 88.28403 92.46301 94.41697 assigned negative charge : -416.3312 centred at (gu) : 87.52387 92.02997 94.51211 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 86579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24058 grid for indexing accessible points = 1.400000 m= 33871 mr = 60774 m= 5738 mr = 25583 m= 439 mr = 3675 m= 11 mr = 205 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1193 time to turn everything in is 0.6800000 number of dielectric boundary points 36401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20520 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) : 0.6606295 object centre at (A) : 13.46000 -3.027000 18.66900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1872887E-02 8.9417892E-03 midg,1,midg; midg,igrid,midg -1.8592857E-02 1.0922393E-02 1,midg,midg; igrid,midg,midg -2.7156696E-02 5.8246739E-02 gauss-seidel spectral radius is 0.9987518 estimated iterations to convergence 224 setup time was (sec) 0.9700000 now iterating at: 03:57:15 rms-change max change #iterations 4.835077 238.5519 at 10iterations 2.343605 75.46786 at 20iterations 1.136318 35.52066 at 30iterations 0.5511094 16.26724 at 40iterations 0.2671080 8.406702 at 50iterations 0.1295784 4.224758 at 60iterations 6.2914424E-02 1.810165 at 70iterations 3.0504124E-02 0.9452171 at 80iterations 1.4812248E-02 0.4830294 at 90iterations 7.1680276E-03 0.2183990 at 100iterations 3.4781124E-03 9.4703674E-02 at 110iterations 1.6895689E-03 4.7651291E-02 at 120iterations finished qdiffx linear iterations at : 03:57:25 total time elapsed so far: 10.82000 # loops : 120 mean,max change (kT/e) : 1.6895689E-03 4.7651291E-02 energy calculations done at 10.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.98000 DelPhi exited at 03:57:26 10.988u 0.444s 0:12.26 93.1% 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 Tue Oct 11 2011 at 03:57:26 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 2.972832 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): -9.723000 36.64300 ymin,ymax (A): -27.67400 21.62000 zmin,zma (A): -8.275000 45.61300 x,y,z range (A): 46.36600 49.29400 53.88800 scale (grids/A): 2.972832 object centre (A): 13.46000 -3.027000 18.66900 number of atom coordinates read : 2700 total number of charged atoms : 2598 net assigned charge : 3.926016 assigned positive charge : 420.2567 centred at (gu) : 87.42596 93.69437 96.62543 assigned negative charge : -416.3312 centred at (gu) : 86.28568 93.04491 96.76814 start vw surface at 0.1200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 199674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24058 grid for indexing accessible points = 1.400000 m= 107270 mr = 146624 m= 41348 mr = 88987 m= 10505 mr = 33686 m= 1800 mr = 8050 m= 159 mr = 1262 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 3997 time to turn everything in is 1.820000 number of dielectric boundary points 82063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 20779 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) : 1.981888 object centre at (A) : 13.46000 -3.027000 18.66900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1767415 0.2598190 midg,1,midg; midg,igrid,midg -0.2246832 5.1322807E-02 1,midg,midg; igrid,midg,midg -0.2319169 0.5099518 gauss-seidel spectral radius is 0.9992961 estimated iterations to convergence 297 setup time was (sec) 2.150000 now iterating at: 03:57:28 rms-change max change #iterations 11.12256 429.3848 at 10iterations 6.614884 145.2313 at 20iterations 3.917136 88.35413 at 30iterations 2.311792 56.01738 at 40iterations 1.361172 30.26014 at 50iterations 0.8014902 14.74789 at 60iterations 0.4709948 7.781065 at 70iterations 0.2764674 4.988976 at 80iterations 0.1617757 2.884359 at 90iterations 9.4633423E-02 1.566345 at 100iterations 5.5321991E-02 1.008301 at 110iterations 3.2343626E-02 0.5644875 at 120iterations 1.8917987E-02 0.3306990 at 130iterations 1.1030724E-02 0.1881866 at 140iterations 6.4561078E-03 0.1045742 at 150iterations 3.7662683E-03 7.1268082E-02 at 160iterations 2.2007353E-03 3.9655924E-02 at 170iterations 1.2869495E-03 2.4024963E-02 at 180iterations finished qdiffx linear iterations at : 03:57:42 total time elapsed so far: 15.88000 # loops : 180 mean,max change (kT/e) : 1.2869495E-03 2.4024963E-02 energy calculations done at 15.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.04000 DelPhi exited at 03:57:43 16.050u 0.452s 0:17.05 96.7% 0+0k 0+0io 0pf+0w