Recently I was dealing with a nice literature, in which the authors have provided an optimized structure of L-DOPA in a GAUSSIAN archived entry file. Can I convert the file into .mol format?
The file is attached herewith.
A few ways do deal with that problem. Let's take 2.1.1. from your file as an example, which starts with:
N-N= 8.932445787130D+02 E-N=-3.422399794402D+03 KE= 7.031766583612D+02
1|1|UNPC-UNK|SP|RB3LYP|6-311G(d,p)|C9H12N1O4(1+)|PCUSER|19-Sep-2011|0|
|# B3LYP/6-311G(D,P) SCRF=(CPCM,READ)||L-DOPA(NH3)||1,1|C,0,2.06819763
82,-2.2082816197,0.0051633082|C,0,0.9210740586,-2.4426059185,-0.739655
1. Manually. You can easily prepare a .xyz file. Open a new file in any editor (text-based, like notepad, vi or someting similar). The coordinates of this system start after the ||1,1|. So the first atom is carbon (C) and has xyz coordinates 2.0681976382, -2.2082816197 and 0.0051633082 (skip the first 0 after C and comma). Put that into your file in one line as:
C 2.0681976382 -2.2082816197 0.0051633082
Do the same with all other coordinates, each in a new line, until you reach the last atom (before ||Version). Add two more lines at the beginnign of this file - first, with the number of atoms and second, completely blank, fir this example:
26
C 2.0681976382 -2.2082816197 0.0051633082
...
You just obtained a good .xyz file, which you can convert to .mol format using e.g. OpenBabel.
2. Using a short script I just made (Linux/Unix only). Save the coordinates from the archive file into any file (e.g. test.arch). Just the coordinates, so in your example: C,0,2.06819763
82,-2.2082816197,0.0051633082|C,0,0.9210740586,-2.4426059185,-0.739655
8029|C,0,0.0588397984,-1.379100534,-1.0501533139|C,0,0.3544189679,-0.0
776158378,-0.6187101575|C,0,1.51220816,0.1493766253,0.143835513|C,0,2.
3721032419,-0.8993045601,0.4515910467|C,0,-0.6009432756,1.0585079213,-
0.9094329513|C,0,-1.4961527414,1.3776367548,0.3206393608|N,0,-2.149632
942,0.1032403565,0.8128382381|O,0,3.4853315767,-0.6622427152,1.1745895
957|O,0,2.9841443788,-3.1493246473,0.3706367671|C,0,-2.6546329475,2.31
18899713,-0.0263638661|O,0,-2.2344090965,3.5512961265,-0.2402149028|O,
0,-3.7951540332,1.9072824194,-0.1214786611|H,0,0.700425679,-3.44514763
51,-1.0976377867|H,0,-0.7981265601,-1.5648883074,-1.6944472497|H,0,1.7
821293719,1.145797565,0.4832239394|H,0,-1.2444620606,0.812526299,-1.76
2573313|H,0,-0.0736122043,1.9839104093,-1.1604322542|H,0,-0.8917790696
,1.7832248607,1.1340854169|H,0,-2.9954303617,4.1086318985,-0.501563270
3|H,0,-1.587335131,-0.7125929014,0.4998966174|H,0,-3.1072109541,0.0807
900945,0.4140176183|H,0,2.7834924027,-4.0109021542,-0.0277436305|H,0,3
.9869808246,-1.4931433367,1.2600086494|H,0,-2.2376213518,0.0700044285,
1.833556383
The do the following command:
sed ':a;N;$!ba;s/\n//g;s/ //g;s/,0,/ /g;s/|/\n/g;s/,/ /g' test.arch > test.xyz
It will produce a test.xyz file with proper formatting, just as in no 1. Add the first two lines as above (no of atoms and blank line) and convert it to .mol using OpenBabel.
Can I do it in windows? I am a newbie in DFT and this is a bit hard for me.
Probably, there's a sed version for windows. But sed it's just a simple replacement tool (well, kind of simple), and you can do that in any good windows text editor. So:
1. Open an empty text file (even Notepad will do) and copy the coordinates, as in point 2 above.
2. Delete all newlines so the entire text is in one line.
3. Replace every | with a new line.
4. Replace every ,0, with a space
5. Replace every , with a space
And you're done and have a good .xyz file, after you add the first two lines.
Also, the manual preparation, as described above in point 1 would also work fine. It's just a bit of manual editing, shouldn't take more than a few minutes for each structure.
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