Sat Oct 8 15:13:50 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 15:13:50 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3256 !!! WARNING: SEP 419 has a net charge of -0.4750 !!! WARNING: GLM 475 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6448107 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): 4.508000 59.11700 ymin,ymax (A): 2.927000 58.13700 zmin,zma (A): -61.16600 -9.298000 x,y,z range (A): 54.60900 55.21000 51.86800 scale (grids/A): 0.6448107 object centre (A): 31.81250 30.53200 -35.23200 number of atom coordinates read : 3256 total number of charged atoms : 3103 net assigned charge : 1.431008 assigned positive charge : 487.6218 centred at (gu) : 91.65096 90.86753 91.26414 assigned negative charge : -486.1921 centred at (gu) : 91.64846 90.81866 91.26701 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9191 nv = 96 ne = 84 npr = 66936 no. pairs analyzed = 66936 no. exposed pairs = 3754 no. arc points = 25911 no. surface atoms = 1279 nbur = 1977 mkacc time = 0.2200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 5353 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.4600000 number of dielectric boundary points 4249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2551 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 10988 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1377753E-09 2.3563551E-09 midg,1,midg; midg,igrid,midg -4.8194169E-09 1.2467230E-08 1,midg,midg; igrid,midg,midg 1.3542046E-09 3.8236205E-09 gauss-seidel spectral radius is 0.9875944 estimated iterations to convergence 73 setup time was (sec) 0.8100000 now iterating at: 15:13:51 rms-change max change #iterations 0.1692267 23.01859 at 10iterations 1.7507924E-02 2.515827 at 20iterations 1.8096471E-03 0.2108192 at 30iterations 1.9180561E-04 2.3500443E-02 at 40iterations 2.4219706E-05 2.8915405E-03 at 50iterations finished qdiffx linear iterations at : 15:13:55 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 2.4219706E-05 2.8915405E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 15:13:55 4.536u 0.426s 0:05.24 94.4% 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 15:13:55 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3256 !!! WARNING: SEP 419 has a net charge of -0.4750 !!! WARNING: GLM 475 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.934432 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): 4.508000 59.11700 ymin,ymax (A): 2.927000 58.13700 zmin,zma (A): -61.16600 -9.298000 x,y,z range (A): 54.60900 55.21000 51.86800 scale (grids/A): 1.934432 object centre (A): 31.81250 30.53200 -35.23200 number of atom coordinates read : 3256 total number of charged atoms : 3103 net assigned charge : 1.431008 assigned positive charge : 487.6218 centred at (gu) : 94.95213 92.60178 93.79142 assigned negative charge : -486.1921 centred at (gu) : 94.94520 92.45559 93.80066 start vw surface at 0.1900000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 99749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25911 grid for indexing accessible points = 1.400000 m= 36736 mr = 71883 m= 5553 mr = 27684 m= 276 mr = 3543 m= 2 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 523 time to turn everything in is 0.9900000 number of dielectric boundary points 39116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 24433 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) : 0.6448107 object centre at (A) : 31.81250 30.53200 -35.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3631297E-03 8.7988313E-04 midg,1,midg; midg,igrid,midg -4.0533058E-02 -6.0589075E-02 1,midg,midg; igrid,midg,midg 2.5448106E-02 2.6940543E-02 gauss-seidel spectral radius is 0.9987327 estimated iterations to convergence 222 setup time was (sec) 1.330000 now iterating at: 15:13:57 rms-change max change #iterations 4.997303 180.1329 at 10iterations 2.413625 75.28709 at 20iterations 1.163951 31.88314 at 30iterations 0.5608927 16.84494 at 40iterations 0.2697822 7.898526 at 50iterations 0.1299680 3.831249 at 60iterations 6.2958643E-02 1.764895 at 70iterations 3.0260583E-02 0.8825127 at 80iterations 1.4601890E-02 0.4065232 at 90iterations 7.0351548E-03 0.2167959 at 100iterations 3.3949632E-03 8.8536263E-02 at 110iterations 1.6461206E-03 4.7180891E-02 at 120iterations finished qdiffx linear iterations at : 15:14:09 total time elapsed so far: 13.08000 # loops : 120 mean,max change (kT/e) : 1.6461206E-03 4.7180891E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 15:14:09 13.295u 0.435s 0:14.01 97.9% 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 15:14:09 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3256 !!! WARNING: SEP 419 has a net charge of -0.4750 !!! WARNING: GLM 475 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.901648 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): 4.508000 59.11700 ymin,ymax (A): 2.927000 58.13700 zmin,zma (A): -61.16600 -9.298000 x,y,z range (A): 54.60900 55.21000 51.86800 scale (grids/A): 2.901648 object centre (A): 31.81250 30.53200 -35.23200 number of atom coordinates read : 3256 total number of charged atoms : 3103 net assigned charge : 1.431008 assigned positive charge : 487.6218 centred at (gu) : 97.42809 93.90250 95.68707 assigned negative charge : -486.1921 centred at (gu) : 97.41776 93.68325 95.70091 start vw surface at 0.1800000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 230852 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25911 grid for indexing accessible points = 1.400000 m= 120217 mr = 173429 m= 42774 mr = 100260 m= 10050 mr = 34699 m= 1303 mr = 7717 m= 58 mr = 882 m= 0 mr = 21 time to grow re-entrant surface = 1.600000 no. cavity mid-points inaccessible to solvent = 1764 time to turn everything in is 2.600000 number of dielectric boundary points 88246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.780000 number of grid points assigned charge 24823 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) : 1.934432 object centre at (A) : 31.81250 30.53200 -35.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7891303E-02 -0.2455828 midg,1,midg; midg,igrid,midg -0.2711682 -0.9133905 1,midg,midg; igrid,midg,midg 0.3090281 0.1695093 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.990000 now iterating at: 15:14:13 rms-change max change #iterations 11.55275 379.1267 at 10iterations 6.832274 132.1056 at 20iterations 4.031816 68.73140 at 30iterations 2.374761 45.81866 at 40iterations 1.395343 24.14105 at 50iterations 0.8183960 13.19174 at 60iterations 0.4791256 7.628708 at 70iterations 0.2803955 4.635244 at 80iterations 0.1641801 2.693900 at 90iterations 9.5932871E-02 1.660904 at 100iterations 5.6176320E-02 0.8870685 at 110iterations 3.2879252E-02 0.5149689 at 120iterations 1.9189233E-02 0.3270226 at 130iterations 1.1251489E-02 0.1669879 at 140iterations 6.6034826E-03 0.1078129 at 150iterations 3.8771476E-03 5.5961609E-02 at 160iterations 2.2855345E-03 3.6599159E-02 at 170iterations 1.3603151E-03 2.4614334E-02 at 180iterations finished qdiffx linear iterations at : 15:14:30 total time elapsed so far: 19.71000 # loops : 180 mean,max change (kT/e) : 1.3603151E-03 2.4614334E-02 energy calculations done at 19.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.94000 DelPhi exited at 15:14:30 19.944u 0.481s 0:20.72 98.5% 0+0k 0+0io 0pf+0w