Tue Oct 11 01:09:35 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 01:09:35 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6193243 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): -6.046000 51.43600 ymin,ymax (A): -15.90700 28.58500 zmin,zma (A): 58.66600 110.9410 x,y,z range (A): 57.48200 44.49200 52.27500 scale (grids/A): 0.6193243 object centre (A): 22.69500 6.339001 84.80350 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 4.312016 assigned positive charge : 412.1376 centred at (gu) : 89.90374 90.29776 89.47846 assigned negative charge : -407.8262 centred at (gu) : 90.17307 90.20747 89.49599 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6965 nv = 96 ne = 84 npr = 55357 no. pairs analyzed = 55357 no. exposed pairs = 3198 no. arc points = 22814 no. surface atoms = 1084 nbur = 1649 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 343 mr = 3943 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 125 time to turn everything in is 0.3400000 number of dielectric boundary points 3330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2169 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8496 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1312510E-09 1.9581583E-09 midg,1,midg; midg,igrid,midg -2.6696199E-09 1.0155245E-08 1,midg,midg; igrid,midg,midg 2.1753351E-08 -1.5302861E-08 gauss-seidel spectral radius is 0.9865085 estimated iterations to convergence 70 setup time was (sec) 0.6000000 now iterating at: 01:09:36 rms-change max change #iterations 0.1352829 18.75957 at 10iterations 1.2981558E-02 2.052979 at 20iterations 1.6182212E-03 0.3081093 at 30iterations 3.7856697E-04 8.5170746E-02 at 40iterations 1.0600927E-04 2.4902344E-02 at 50iterations finished qdiffx linear iterations at : 01:09:39 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.0600927E-04 2.4902344E-02 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 01:09:40 3.642u 0.201s 0:04.24 90.5% 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 Tue Oct 11 2011 at 01:09:40 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.857973 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): -6.046000 51.43600 ymin,ymax (A): -15.90700 28.58500 zmin,zma (A): 58.66600 110.9410 x,y,z range (A): 57.48200 44.49200 52.27500 scale (grids/A): 1.857973 object centre (A): 22.69500 6.339001 84.80350 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 4.312016 assigned positive charge : 412.1376 centred at (gu) : 89.71039 90.89282 88.43477 assigned negative charge : -407.8262 centred at (gu) : 90.51880 90.62218 88.48762 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22814 grid for indexing accessible points = 1.400000 m= 26651 mr = 53410 m= 3887 mr = 19919 m= 176 mr = 2382 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 3938 time to turn everything in is 0.5600000 number of dielectric boundary points 30897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20223 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) : 0.6193243 object centre at (A) : 22.69500 6.339001 84.80350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7373009E-04 6.3123200E-03 midg,1,midg; midg,igrid,midg 9.2243841E-03 1.7336257E-02 1,midg,midg; igrid,midg,midg 3.7654791E-02 -3.7296079E-02 gauss-seidel spectral radius is 0.9985791 estimated iterations to convergence 210 setup time was (sec) 0.8800000 now iterating at: 01:09:41 rms-change max change #iterations 4.151822 174.0038 at 10iterations 1.903680 73.76016 at 20iterations 0.8780118 33.08071 at 30iterations 0.4046410 13.94111 at 40iterations 0.1867841 6.287781 at 50iterations 8.6540304E-02 2.657875 at 60iterations 3.9971661E-02 1.254333 at 70iterations 1.8589890E-02 0.5949020 at 80iterations 8.7164026E-03 0.2693558 at 90iterations 4.1353269E-03 0.1594734 at 100iterations 2.0394640E-03 7.8214645E-02 at 110iterations 1.0603856E-03 3.9470673E-02 at 120iterations finished qdiffx linear iterations at : 01:09:48 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 1.0603856E-03 3.9470673E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 01:09:49 8.231u 0.224s 0:09.01 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 Tue Oct 11 2011 at 01:09:49 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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: 2.786959 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): -6.046000 51.43600 ymin,ymax (A): -15.90700 28.58500 zmin,zma (A): 58.66600 110.9410 x,y,z range (A): 57.48200 44.49200 52.27500 scale (grids/A): 2.786959 object centre (A): 22.69500 6.339001 84.80350 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 4.312016 assigned positive charge : 412.1376 centred at (gu) : 89.56545 91.33902 87.65205 assigned negative charge : -407.8262 centred at (gu) : 90.77814 90.93315 87.73145 start vw surface at 0.2000000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 175799 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22814 grid for indexing accessible points = 1.400000 m= 87906 mr = 129438 m= 30267 mr = 72474 m= 6815 mr = 24531 m= 865 mr = 5171 m= 32 mr = 559 m= 0 mr = 7 time to grow re-entrant surface = 0.8199999 no. cavity mid-points inaccessible to solvent = 13596 time to turn everything in is 1.450000 number of dielectric boundary points 69504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 20648 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) : 1.857973 object centre at (A) : 22.69500 6.339001 84.80350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2327861E-02 3.3724722E-02 midg,1,midg; midg,igrid,midg 0.1490787 0.2071522 1,midg,midg; igrid,midg,midg 0.4204385 -0.3528360 gauss-seidel spectral radius is 0.9992400 estimated iterations to convergence 286 setup time was (sec) 1.780000 now iterating at: 01:09:51 rms-change max change #iterations 9.839005 349.6895 at 10iterations 5.703116 124.8345 at 20iterations 3.288607 68.00018 at 30iterations 1.884100 35.05111 at 40iterations 1.081352 19.67713 at 50iterations 0.6186818 11.40930 at 60iterations 0.3542715 6.700401 at 70iterations 0.2020688 3.682728 at 80iterations 0.1155214 2.516936 at 90iterations 6.6149794E-02 1.145994 at 100iterations 3.7740555E-02 0.6968765 at 110iterations 2.1614054E-02 0.3884277 at 120iterations 1.2445944E-02 0.2294464 at 130iterations 7.2299237E-03 0.1364136 at 140iterations 4.2526410E-03 8.1367493E-02 at 150iterations 2.5679336E-03 5.6941986E-02 at 160iterations 1.6150401E-03 3.8417816E-02 at 170iterations 1.0752050E-03 2.7545929E-02 at 180iterations finished qdiffx linear iterations at : 01:10:01 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 1.0752050E-03 2.7545929E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 01:10:02 12.379u 0.242s 0:13.08 96.4% 0+0k 0+0io 0pf+0w