Sat Oct 15 11:54:06 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 15 2011 at 11:54:06 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2427 !!! WARNING: ASL 1112 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5936698 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): 8.474000 64.66400 ymin,ymax (A): 13.29300 59.46400 zmin,zma (A): -30.07300 29.89300 x,y,z range (A): 56.19000 46.17100 59.96600 scale (grids/A): 0.5936698 object centre (A): 36.56900 36.37850 -9.0000153E-02 number of atom coordinates read : 2427 total number of charged atoms : 2287 net assigned charge : 2.900012 assigned positive charge : 361.2065 centred at (gu) : 89.66705 89.92664 89.20190 assigned negative charge : -358.3070 centred at (gu) : 89.41434 89.72757 89.03758 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5875 nv = 96 ne = 84 npr = 46735 no. pairs analyzed = 46735 no. exposed pairs = 3433 no. arc points = 24828 no. surface atoms = 1143 nbur = 1284 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 265 mr = 2805 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2800000 number of dielectric boundary points 3324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2382 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7190 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2634958E-09 4.6195145E-09 midg,1,midg; midg,igrid,midg -4.6049489E-09 6.3610122E-09 1,midg,midg; igrid,midg,midg -6.5852244E-09 7.2911490E-09 gauss-seidel spectral radius is 0.9853177 estimated iterations to convergence 68 setup time was (sec) 0.4900000 now iterating at: 11:54:07 rms-change max change #iterations 9.6380621E-02 15.17127 at 10iterations 8.0185635E-03 1.478572 at 20iterations 6.7338895E-04 0.1020012 at 30iterations 7.1183400E-05 1.2011051E-02 at 40iterations 2.2162802E-05 4.2676926E-03 at 50iterations finished qdiffx linear iterations at : 11:54:09 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 2.2162802E-05 4.2676926E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 11:54:10 3.109u 0.140s 0:03.66 88.5% 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 Sat Oct 15 2011 at 11:54:10 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2427 !!! WARNING: ASL 1112 has a net charge of -0.1000 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: 1.781009 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): 8.474000 64.66400 ymin,ymax (A): 13.29300 59.46400 zmin,zma (A): -30.07300 29.89300 x,y,z range (A): 56.19000 46.17100 59.96600 scale (grids/A): 1.781009 object centre (A): 36.56900 36.37850 -9.0000153E-02 number of atom coordinates read : 2427 total number of charged atoms : 2287 net assigned charge : 2.900012 assigned positive charge : 361.2065 centred at (gu) : 89.00081 89.77946 87.60511 assigned negative charge : -358.3070 centred at (gu) : 88.24300 89.18254 87.11270 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 63817 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24828 grid for indexing accessible points = 1.400000 m= 20824 mr = 41219 m= 2814 mr = 13971 m= 136 mr = 1466 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 30894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 17780 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) : 0.5936698 object centre at (A) : 36.56900 36.37850 -9.0000153E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1479982E-02 4.9599729E-02 midg,1,midg; midg,igrid,midg -2.0111389E-02 1.9452911E-02 1,midg,midg; igrid,midg,midg -2.7123507E-02 8.3083026E-03 gauss-seidel spectral radius is 0.9984440 estimated iterations to convergence 201 setup time was (sec) 0.7200000 now iterating at: 11:54:11 rms-change max change #iterations 3.538568 161.2531 at 10iterations 1.574423 65.32475 at 20iterations 0.6963831 28.90424 at 30iterations 0.3078671 11.84062 at 40iterations 0.1368143 5.184298 at 50iterations 6.0773529E-02 2.360435 at 60iterations 2.6923424E-02 0.9310951 at 70iterations 1.1944328E-02 0.4207592 at 80iterations 5.3137289E-03 0.1895256 at 90iterations 2.3636632E-03 8.7669373E-02 at 100iterations 1.0498975E-03 3.8387537E-02 at 110iterations 4.6614729E-04 1.6765594E-02 at 120iterations finished qdiffx linear iterations at : 11:54:17 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 4.6614729E-04 1.6765594E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.020000 DelPhi exited at 11:54:17 7.025u 0.151s 0:07.55 94.9% 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 15 2011 at 11:54:17 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2427 !!! WARNING: ASL 1112 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.671514 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): 8.474000 64.66400 ymin,ymax (A): 13.29300 59.46400 zmin,zma (A): -30.07300 29.89300 x,y,z range (A): 56.19000 46.17100 59.96600 scale (grids/A): 2.671514 object centre (A): 36.56900 36.37850 -9.0000153E-02 number of atom coordinates read : 2427 total number of charged atoms : 2287 net assigned charge : 2.900012 assigned positive charge : 361.2065 centred at (gu) : 88.50110 89.66905 86.40770 assigned negative charge : -358.3070 centred at (gu) : 87.36447 88.77374 85.66904 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 147688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24828 grid for indexing accessible points = 1.400000 m= 68561 mr = 101098 m= 22546 mr = 52885 m= 4614 mr = 16824 m= 588 mr = 3127 m= 30 mr = 347 m= 0 mr = 20 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 69726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 18294 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) : 1.781009 object centre at (A) : 36.56900 36.37850 -9.0000153E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1921367 0.7412653 midg,1,midg; midg,igrid,midg -0.2638451 0.2390660 1,midg,midg; igrid,midg,midg -0.3381482 7.0262440E-02 gauss-seidel spectral radius is 0.9992131 estimated iterations to convergence 281 setup time was (sec) 1.380000 now iterating at: 11:54:19 rms-change max change #iterations 8.769733 293.9075 at 10iterations 5.091217 130.1571 at 20iterations 2.928287 85.02879 at 30iterations 1.681135 37.25014 at 40iterations 0.9611321 24.27951 at 50iterations 0.5472556 11.91983 at 60iterations 0.3108355 6.544556 at 70iterations 0.1769802 3.596132 at 80iterations 0.1002454 1.983444 at 90iterations 5.6791939E-02 1.145745 at 100iterations 3.2161091E-02 0.6902066 at 110iterations 1.8261099E-02 0.3720284 at 120iterations 1.0314506E-02 0.2249250 at 130iterations 5.8497586E-03 0.1192336 at 140iterations 3.3031232E-03 6.9290102E-02 at 150iterations 1.8682641E-03 3.5404205E-02 at 160iterations 1.0552647E-03 2.2318125E-02 at 170iterations 5.9801288E-04 1.2527466E-02 at 180iterations finished qdiffx linear iterations at : 11:54:29 total time elapsed so far: 10.99000 # loops : 180 mean,max change (kT/e) : 5.9801288E-04 1.2527466E-02 energy calculations done at 10.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.17000 DelPhi exited at 11:54:29 11.168u 0.173s 0:11.84 95.6% 0+0k 0+0io 0pf+0w