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)
Code:
ATOM 1 C1 C20 P 1 1.000 1.540 0.000 1.00 0.00 C
ATOM 2 C2 C20 P 1 2.456 2.041 0.000 1.00 0.00 C
ATOM 7 C1 C20 P 1 2.456 3.581 0.000 1.00 0.00 C
ATOM 8 C2 C20 P 1 3.912 4.083 -0.000 1.00 0.00 C
ATOM 13 C1 C20 P 1 3.912 5.623 -0.000 1.00 0.00 C
ATOM 14 C2 C20 P 1 5.368 6.124 -0.000 1.00 0.00 C
ATOM 19 C1 C20 P 1 5.368 7.664 -0.000 1.00 0.00 C
ATOM 20 C2 C20 P 1 6.824 8.165 -0.000 1.00 0.00 C
ATOM 25 C1 C20 P 1 6.824 9.705 -0.000 1.00 0.00 C
ATOM 26 C2 C20 P 1 8.280 10.207 -0.000 1.00 0.00 C
The output file needs to be modified into the following format,
Code:
ATOM 1 CM ETH P 1 1.000 1.540 0.000 1.00 0.00 C
ATOM 2 CD ETH P 1 2.456 2.041 0.000 1.00 0.00 C
ATOM 3 CM ETH P 2 2.456 3.581 0.000 1.00 0.00 C
ATOM 4 CD ETH P 2 3.912 4.083 -0.000 1.00 0.00 C
ATOM 5 CM ETH P 3 3.912 5.623 -0.000 1.00 0.00 C
ATOM 6 CD ETH P 3 5.368 6.124 -0.000 1.00 0.00 C
ATOM 7 CM ETH P 4 5.368 7.664 -0.000 1.00 0.00 C
ATOM 8 CD ETH P 4 6.824 8.165 -0.000 1.00 0.00 C
ATOM 9 CM ETH P 5 6.824 9.705 -0.000 1.00 0.00 C
ATOM 10 CD ETH P 5 8.280 10.207 -0.000 1.00 0.00 C
TER 11
CONECT 1
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3 5
CONECT 5 4 6
CONECT 6 5 7
CONECT 7 6 8
CONECT 8 7 9
CONECT 9 8 10
CONECT 10 9
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..
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