Hmmm, I think I found a logical error in my proposal: adding the $i after the awk script made it immediately read the respective .pdb file, not voronota's output from that file. Remove the $i:
and report back.
Still, I'm convinced there will be an apter / better solution to the overall problem dealing with ALL .pdb files, and ALL amino acids in one go if needed...
And, please use CODE, not ICODE, tags for data as well. You may want to edit your former post.
I was wondering if it was possible to tell awk to print the output of a command in the print.
.... | awk '{print $0}'
I would like it to print the date right before $0, so something like (this doesn't work though)
.... | awk '{print date $0}' (4 Replies)
Hi, I'm stuck in an awkward situation please help :)
I have two identical Seagate 80GB harddrives.
My objective is a bit strange.
1.I want to have a cloned disk as bootable backup
2.When booting using the master drive, I also want to mount the cloned backup disk so I can do incremental... (6 Replies)
I have a file, let's say 1.jpg, and I have a text file that contains a list of filenames I would like to duplicate 1.jpg as (i.e., 2.jpg, 3.jpg, 4.jpg, etc.). The filenames that I want to create are all on separate lines, one per line.
I'm sure there's a simple solution, but I'm not claiming to... (7 Replies)
Hi all,
Actually 2 files are there - file1, file2.
file1 contains --->
london
mosco
america
russia
mosco
file2 contains -->
europe
india
japan
mosco
england
london
Question is I want to print all the city names without duplication cities in those... (10 Replies)
i have many questions concerning the FD.
it was stated that "to redirect Error to output std, you have to write the following code"
# ls -alt FileNotThere File > logfile 2>&1
# cat logfile
ls: cannot access FileNotThere: No such file or directory
-rw-r--r-- 1 root root 0 2010-02-26... (9 Replies)
Hey,
I am making a Facebook like Page system as my first project, So far it's been bate in mind I did it from my 3DS at the same time as my PC gets replaced, So far it's turned out great. Now I am on to creation the blocking system I need to get the code to say If the user already likes the... (0 Replies)
Hi all,
I download and install lessfs for deduplication,
I copy files in /SharedFiles directory and lessfs work right and not store again copy files,
but, when i delete all files in /SharedFiles , not return free space to total space,
files not show in /SharedFiles , but not copy new files in... (3 Replies)
So while this seemed totally trivial it turned out to be much more difficult than I had thought.
I have a file with 3 rows, and I "just" want to add each field n number of times. E.g.
> cat file.txt
0.5
-0.1
0.6
for n=3 into:
cat newfile.txt
0.5 0.5 0.5
-0.1 -0.1 -0.1
0.6 0.6 0.6
I... (4 Replies)
Hello,
Giving those commands:
cat > myfile
1
2
3
^D
cat myfile | awk '{ s=s+$1 ; print s}'
The output is:
1
3
6
It seems like this command iterates each time on a different row so $1 is the first field of each row.. But what caused it to refer to each row ?.
What I mean... (3 Replies)
Discussion started by: uniran
3 Replies
LEARN ABOUT DEBIAN
g_confrms
g_confrms(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_confrms(1)NAME
g_confrms - fits two structures and calculates the rmsd
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_confrms -f1 conf1.gro -f2 conf2.gro -o fit.pdb -n1 fit1.ndx -n2 fit2.ndx -no match.ndx -[no]h -[no]version -nice int -[no]w -[no]one
-[no]mw -[no]pbc -[no]fit -[no]name -[no]label -[no]bfac
DESCRIPTION
g_confrms computes the root mean square deviation (RMSD) of two structures after least-squares fitting the second structure on the first
one. The two structures do NOT need to have the same number of atoms, only the two index groups used for the fit need to be identical.
With -name only matching atom names from the selected groups will be used for the fit and RMSD calculation. This can be useful when com-
paring mutants of a protein.
The superimposed structures are written to file. In a .pdb file the two structures will be written as separate models (use rasmol -nmr-
pdb). Also in a .pdb file, B-factors calculated from the atomic MSD values can be written with -bfac.
FILES -f1 conf1.gro Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-f2 conf2.gro Input
Structure file: gro g96 pdb tpr etc.
-o fit.pdb Output
Structure file: gro g96 pdb etc.
-n1 fit1.ndx Input, Opt.
Index file
-n2 fit2.ndx Input, Opt.
Index file
-no match.ndx Output, Opt.
Index file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 19
Set the nicelevel
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-[no]oneno
Only write the fitted structure to file
-[no]mwyes
Mass-weighted fitting and RMSD
-[no]pbcno
Try to make molecules whole again
-[no]fityes
Do least squares superposition of the target structure to the reference
-[no]nameno
Only compare matching atom names
-[no]labelno
Added chain labels A for first and B for second structure
-[no]bfacno
Output B-factors from atomic MSD values
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_confrms(1)