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)