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Full Discussion: How to insert something to a file from another file with shell?
Top Forums Shell Programming and Scripting How to insert something to a file from another file with shell? Post 303007250 by 510426762 on Tuesday 14th of November 2017 12:33:48 PM
Old 11-14-2017
How to insert something to a file from another file with shell?
complex.gro
Code:
Great Red Owns Many ACres of Sand 
 6340
    6SER      N    1   2.724  13.826   0.957
    6SER     H1    2   2.685  13.863   1.041
    6SER     H2    3   2.783  13.748   0.979
   .
   .
   .
  405TYR      C 6338   4.079  11.113   0.908
  405TYR    OC1 6339   4.166  11.065   0.896
  405TYR    OC2 6340   4.045  11.204   0.829
   8.10576   5.73277   5.32581


lig.gro
Code:
MOL_GMX.gro created by acpype (Rev: 10101) on Tue Nov 14 21:43:44 2017
 37
    1  MOL   C1    1   5.094  10.087   2.868
    1  MOL   C2    2   4.998  10.172   2.807
    1  MOL   C3    3   4.940  10.136   2.690
   .
   .
   .
    1  MOL  H15   35   5.432  10.090   3.227
    1  MOL  H16   36   5.389  10.124   2.993
    1  MOL  H17   37   5.482   9.982   2.948
   15.26200    11.53200    18.72600

I want insert the red part of lig.gro in the complex.gro before the last line
and
change the 2nd line number in complex.gro(6340+37)

the result is like next
complex.gro
Code:
Great Red Owns Many ACres of Sand 
 6377
    6SER      N    1   2.724  13.826   0.957
    6SER     H1    2   2.685  13.863   1.041
    6SER     H2    3   2.783  13.748   0.979
   .
   .
   .
  405TYR      C 6338   4.079  11.113   0.908
  405TYR    OC1 6339   4.166  11.065   0.896
  405TYR    OC2 6340   4.045  11.204   0.829
    1  MOL   C1    1   5.094  10.087   2.868
    1  MOL   C2    2   4.998  10.172   2.807
    1  MOL   C3    3   4.940  10.136   2.690
   .
   .
   .
    1  MOL  H15   35   5.432  10.090   3.227
    1  MOL  H16   36   5.389  10.124   2.993
    1  MOL  H17   37   5.482   9.982   2.948
   8.10576   5.73277   5.32581

How can I reach the result by using shell script
Last edited by 510426762; 11-14-2017 at 01:58 PM.. Reason: Removed external links
 

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LEARN ABOUT DEBIAN

genconf

genconf(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					genconf(1)

NAME

       genconf - multiplies a conformation in 'random' orientations

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       genconf	-f  conf.gro  -o  out.gro  -trj  traj.xtc  -[no]h -[no]version -nice int -nbox vector -dist vector -seed int -[no]rot -[no]shuffle
       -[no]sort -block int -nmolat int -maxrot vector -[no]renumber

DESCRIPTION

	genconf multiplies a given coordinate file by simply stacking them on top of each other, like a small child playing  with  wooden  blocks.
       The program makes a grid of  user-defined proportions ( -nbox), and interspaces the grid point with an extra space  -dist.

       When option  -rot is used the program does not check for overlap between molecules on grid points. It is recommended to make the box in the
       input file at least as big as the coordinates + van der Waals radius.

       If the optional trajectory file is given, conformations are not generated, but read from this file and translated  appropriately  to  build
       the grid.

FILES

       -f conf.gro Input
	Structure file: gro g96 pdb tpr etc.

       -o out.gro Output
	Structure file: gro g96 pdb etc.

       -trj traj.xtc Input, Opt.
	Trajectory: xtc trr trj gro g96 pdb cpt

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

       -nbox vector 1 1 1
	Number of boxes

       -dist vector 0 0 0
	Distance between boxes

       -seed int 0
	Random generator seed, if 0 generated from the time

       -[no]rotno
	Randomly rotate conformations

       -[no]shuffleno
	Random shuffling of molecules

       -[no]sortno
	Sort molecules on X coord

       -block int 1
	Divide the box in blocks on this number of cpus

       -nmolat int 3
	Number of atoms per molecule, assumed to start from 0. If you set this wrong, it will screw up your system!

       -maxrot vector 180 180 180
	Maximum random rotation

       -[no]renumberyes
	Renumber residues

KNOWN PROBLEMS

       - The program should allow for random displacement of lattice points.

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							genconf(1)
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