I'm no awk expert but..
Everything works fine here with your input files and guru's awk.
I'm getting header as it should be or ? :
After running the code vs your input (a1 and a2) i'm getting.
Also for generating headers via awk, remove the header from the data and use BEGIN block or put another pair of { } bracers infront of guru's code (you will need to remove header from data first)
Something like :
or
hi,
i am facing a problem in merging two files using awk,
the problem is as stated below,
file1:
A|B|C|D|E|F|G|H|I|1
M|N|O|P|Q|R|S|T|U|2
AA|BB|CC|DD|EE|FF|GG|HH|II|1
....
....
....
file2 :
1|Mn|op|qr (2 Replies)
I'm running on freebsd -- with a default shell of csh.
I have two files named A and B. Each line of each file contains a file name. How can I write a script that removes all the file names in file B from A.
I tried to use perl to create a huge regular expression with "|" separating the file... (2 Replies)
I have 100 data files labelled 250.1.txt through 250.100.txt. The second column of the data files partially match (there is about %90 overlap). Each data file has 4 columns.
I want the merge all these text files by the matching values in the second column. In the output, the first column should... (1 Reply)
Hi,
I have two files that I would like to merge and think that there should be a solution using awk. The files look something like this:
file 1
IDX1 IDY1
IDX2 IDY2
IDX3 IDY3
file 2
IDY1 dataA data1
IDY2 dataB data2
IDY3 dataC data3
Desired output
IDX1 IDY1 dataA data1
IDX2 ... (5 Replies)
I have a need to merge two files on the value of an index column.
input file 1
id filePath MDL_NUMBER
1 MFCD00008104.mol MFCD00008104
2 MFCD00012849.mol MFCD00012849
3 MFCD00037597.mol MFCD00037597
4 MFCD00064558.mol MFCD00064558
5 MFCD00064559.mol MFCD00064559
input file 2
... (9 Replies)
Hi,
I have two files A (2190 rows) and file B (1100 rows). I want to merge the contents of two files based on common field, also I need the unmatched rows from file A
file A:
ABC
XYZ
PQR
file B:
>LMN|chr1:11000-12456:
>ABC|chr15:176578-187678:
>PQR|chr3:14567-15866:
output... (3 Replies)
Hi all,
Say i have multiple files x1 x2 x3 x4, all with common header (date, time, year, age),,
How can I merge them to one singe file "X" in shell scripting
Thanks for your suggestions. (2 Replies)
Hi, I am trying to selectively merge two files based on keys reported in the 1st column.
File1:
#file1-header1
file1-header2
111 qwe rtz uio
198 asd fgh jkl
165 yxc
789 poi uzt rew
89 lkj
File2:
#file2-header2
file2-header2
165 ghz nko2 ... (2 Replies)
Hello,
I have 40 data files where the first three columns are the same (in theory) and the 4th column is different. Here is an example of three files,
file 2: A_f0_r179_pred.txt
Id Group Name E0
1 V N(,)'1 0.2904
2 V N(,)'2 0.3180
3 V N(,)'3 0.3277
4 V N(,)'4 0.3675
5 V N(,)'5 0.3456
... (8 Replies)
Discussion started by: LMHmedchem
8 Replies
LEARN ABOUT DEBIAN
g_x2top
g_x2top(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_x2top(1)NAME
g_x2top - generates a primitive topology from coordinates
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_x2top -f conf.gro -o out.top -r out.rtp -[no]h -[no]version -nice int -ff string -[no]v -nexcl int -[no]H14 -[no]alldih -[no]remdih
-[no]pairs -name string -[no]pbc -[no]pdbq -[no]param -[no]round -kb real -kt real -kp real
DESCRIPTION
g_x2top generates a primitive topology from a coordinate file. The program assumes all hydrogens are present when defining the hybridiza-
tion from the atom name and the number of bonds. The program can also make an .rtp entry, which you can then add to the .rtp database.
When -param is set, equilibrium distances and angles and force constants will be printed in the topology for all interactions. The equi-
librium distances and angles are taken from the input coordinates, the force constant are set with command line options. The force fields
somewhat supported currently are:
G53a5 GROMOS96 53a5 Forcefield (official distribution)
oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
The corresponding data files can be found in the library directory with name atomname2type.n2t. Check Chapter 5 of the manual for more
information about file formats. By default, the force field selection is interactive, but you can use the -ff option to specify one of the
short names above on the command line instead. In that case g_x2top just looks for the corresponding file.
FILES -f conf.gro Input
Structure file: gro g96 pdb tpr etc.
-o out.top Output, Opt.
Topology file
-r out.rtp Output, Opt.
Residue Type file used by pdb2gmx
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-ff string oplsaa
Force field for your simulation. Type "select" for interactive selection.
-[no]vno
Generate verbose output in the top file.
-nexcl int 3
Number of exclusions
-[no]H14yes
Use 3rd neighbour interactions for hydrogen atoms
-[no]alldihno
Generate all proper dihedrals
-[no]remdihno
Remove dihedrals on the same bond as an improper
-[no]pairsyes
Output 1-4 interactions (pairs) in topology file
-name string ICE
Name of your molecule
-[no]pbcyes
Use periodic boundary conditions.
-[no]pdbqno
Use the B-factor supplied in a .pdb file for the atomic charges
-[no]paramyes
Print parameters in the output
-[no]roundyes
Round off measured values
-kb real 400000
Bonded force constant (kJ/mol/nm2)
-kt real 400
Angle force constant (kJ/mol/rad2)
-kp real 5
Dihedral angle force constant (kJ/mol/rad2)
KNOWN PROBLEMS
- The atom type selection is primitive. Virtually no chemical knowledge is used
- Periodic boundary conditions screw up the bonding
- No improper dihedrals are generated
- The atoms to atomtype translation table is incomplete ( atomname2type.n2t file in the data directory). Please extend it and send the
results back to the GROMACS crew.
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_x2top(1)