I'm struggling to preparing a bunch of gromacs input files, say manually. It's really a time-consuming work without any techniques. I suppose that it could be done by a smart script automatically. But I lack some basic knowledge on scripting. Please help!
My original input looks like,(only show the first 10 lines, there are a few hundreds of thousands of lines in the input file)
The output file needs to be modified into the following format,
Clearly to say, the script would do:
1. there are 12 columns in each line, keep $1, $5, $7-$12 with no change;
2. ignore the original data in $2, fill with series line number;
3. ignore the original data in $3, fill with series CM CD in the alternative sequence; or just replace C1 with CM and replace C2 with CD;
4. ignore the original data in $4, fill with "ETH"; or simply replace C20 with "ETH"
5. ignore the original data in $6, fill with series 1 1 2 2 3 3 .... up to $(line number)/2;
6. at the end of the output, add some new lines start with "TER LineNum+1";
7. the following line should start with CONECT and fill with three-column numbers of 1-10, 1-9, and 3-10 as shown in the above output sample.
I hope I have already made myself clear in explaining the function of this script. Please do me a favor. All you help will be greatly appreciated. Thank you in advanced!
ZHEN
from Shanghai, China.
Last edited by liuzhencc; 12-07-2014 at 10:52 AM..
Thank you very much, Scrutinizer! it works like a charm! As you metioned, if each column could be printed with format, it'll look much tidy. So, would you please add some function to this script to get the output in the following format?
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