Sat Oct 15 13:13:27 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 13:13:27 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 !!! WARNING: MG7 714 has a net charge of 1.4000 !!! WARNING: MG7 715 has a net charge of 1.4000 !!! WARNING: MG7 716 has a net charge of 1.4000 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: 0.6328214 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): -15.31800 37.64600 ymin,ymax (A): 3.930000 55.86700 zmin,zma (A): -35.58400 20.67200 x,y,z range (A): 52.96400 51.93700 56.25600 scale (grids/A): 0.6328214 object centre (A): 11.16400 29.89850 -7.456000 number of atom coordinates read : 3048 total number of charged atoms : 2895 net assigned charge : -1.487984 assigned positive charge : 452.1852 centred at (gu) : 90.44914 91.27247 89.30591 assigned negative charge : -453.6746 centred at (gu) : 90.41931 91.42090 89.22765 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8244 nv = 96 ne = 84 npr = 61587 no. pairs analyzed = 61587 no. exposed pairs = 3873 no. arc points = 27277 no. surface atoms = 1321 nbur = 1727 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4496 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2664 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1947828E-08 6.1774950E-09 midg,1,midg; midg,igrid,midg 1.1220777E-08 -2.4236421E-08 1,midg,midg; igrid,midg,midg -4.3475827E-09 2.0731123E-09 gauss-seidel spectral radius is 0.9871087 estimated iterations to convergence 72 setup time was (sec) 0.4500000 now iterating at: 13:13:28 rms-change max change #iterations 0.1558200 20.96984 at 10iterations 1.5320188E-02 2.125929 at 20iterations 1.9740062E-03 0.3040161 at 30iterations 5.7301938E-04 9.0209961E-02 at 40iterations 2.4053224E-04 3.4463882E-02 at 50iterations finished qdiffx linear iterations at : 13:13:31 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 2.4053224E-04 3.4463882E-02 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.840000 DelPhi exited at 13:13:32 3.842u 0.233s 0:04.52 90.0% 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 Sat Oct 15 2011 at 13:13:32 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 !!! WARNING: MG7 714 has a net charge of 1.4000 !!! WARNING: MG7 715 has a net charge of 1.4000 !!! WARNING: MG7 716 has a net charge of 1.4000 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: 1.898464 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): -15.31800 37.64600 ymin,ymax (A): 3.930000 55.86700 zmin,zma (A): -35.58400 20.67200 x,y,z range (A): 52.96400 51.93700 56.25600 scale (grids/A): 1.898464 object centre (A): 11.16400 29.89850 -7.456000 number of atom coordinates read : 3048 total number of charged atoms : 2895 net assigned charge : -1.487984 assigned positive charge : 452.1852 centred at (gu) : 91.34657 93.81652 87.91686 assigned negative charge : -453.6746 centred at (gu) : 91.25762 94.26244 87.68266 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 89356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27277 grid for indexing accessible points = 1.400000 m= 31966 mr = 62076 m= 5469 mr = 22957 m= 377 mr = 3366 m= 2 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 268 time to turn everything in is 0.4600000 number of dielectric boundary points 38618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 22716 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) : 0.6328214 object centre at (A) : 11.16400 29.89850 -7.456000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3298986E-02 2.7032077E-02 midg,1,midg; midg,igrid,midg -1.4285195E-03 -2.9227905E-02 1,midg,midg; igrid,midg,midg -1.8162780E-02 -1.2246040E-02 gauss-seidel spectral radius is 0.9986716 estimated iterations to convergence 217 setup time was (sec) 0.7100000 now iterating at: 13:13:33 rms-change max change #iterations 4.652143 171.1052 at 10iterations 2.200181 72.88080 at 20iterations 1.043877 29.61643 at 30iterations 0.4937471 15.02751 at 40iterations 0.2350333 7.051575 at 50iterations 0.1112889 3.350346 at 60iterations 5.2827176E-02 1.553722 at 70iterations 2.5139077E-02 0.7811475 at 80iterations 1.1998048E-02 0.3449955 at 90iterations 5.8148676E-03 0.1633854 at 100iterations 2.8870367E-03 8.2192898E-02 at 110iterations 1.5276923E-03 4.9942017E-02 at 120iterations finished qdiffx linear iterations at : 13:13:41 total time elapsed so far: 8.820000 # loops : 120 mean,max change (kT/e) : 1.5276923E-03 4.9942017E-02 energy calculations done at 8.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.970000 DelPhi exited at 13:13:41 8.969u 0.264s 0:09.50 97.0% 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 Sat Oct 15 2011 at 13:13:41 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 !!! WARNING: MG7 714 has a net charge of 1.4000 !!! WARNING: MG7 715 has a net charge of 1.4000 !!! WARNING: MG7 716 has a net charge of 1.4000 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: 2.847696 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): -15.31800 37.64600 ymin,ymax (A): 3.930000 55.86700 zmin,zma (A): -35.58400 20.67200 x,y,z range (A): 52.96400 51.93700 56.25600 scale (grids/A): 2.847696 object centre (A): 11.16400 29.89850 -7.456000 number of atom coordinates read : 3048 total number of charged atoms : 2895 net assigned charge : -1.487984 assigned positive charge : 452.1852 centred at (gu) : 92.01974 95.72459 86.87531 assigned negative charge : -453.6746 centred at (gu) : 91.88646 96.39351 86.52394 start vw surface at 0.1000000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 207319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27277 grid for indexing accessible points = 1.400000 m= 103236 mr = 151191 m= 37834 mr = 83321 m= 9958 mr = 29807 m= 1675 mr = 7405 m= 82 mr = 1140 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 1026 time to turn everything in is 1.190000 number of dielectric boundary points 87213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 23159 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) : 1.898464 object centre at (A) : 11.16400 29.89850 -7.456000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1969809 0.7076000 midg,1,midg; midg,igrid,midg -0.1515264 -0.3294393 1,midg,midg; igrid,midg,midg -4.4887837E-02 -0.1531527 gauss-seidel spectral radius is 0.9992870 estimated iterations to convergence 295 setup time was (sec) 1.490000 now iterating at: 13:13:43 rms-change max change #iterations 10.99572 363.5013 at 10iterations 6.522673 158.1006 at 20iterations 3.838034 80.46484 at 30iterations 2.259575 53.01571 at 40iterations 1.326159 27.12613 at 50iterations 0.7743262 14.07819 at 60iterations 0.4529104 8.091336 at 70iterations 0.2638447 4.486120 at 80iterations 0.1541680 3.026642 at 90iterations 8.9897849E-02 1.558846 at 100iterations 5.2191496E-02 0.9061432 at 110iterations 3.0482125E-02 0.5205650 at 120iterations 1.7766524E-02 0.2967720 at 130iterations 1.0394404E-02 0.2083616 at 140iterations 6.0921437E-03 0.1090794 at 150iterations 3.6104354E-03 7.1655273E-02 at 160iterations 2.1836839E-03 4.3687820E-02 at 170iterations 1.3676616E-03 2.6124954E-02 at 180iterations finished qdiffx linear iterations at : 13:13:58 total time elapsed so far: 15.36000 # loops : 180 mean,max change (kT/e) : 1.3676616E-03 2.6124954E-02 energy calculations done at 15.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.50000 DelPhi exited at 13:13:58 15.497u 0.317s 0:17.06 92.6% 0+0k 0+0io 0pf+0w