CCL: What is the format of this file containing Cartesian coordinates?
- From: "Tamas Gunda" <tgunda2---puma.unideb.hu>
- Subject: CCL: What is the format of this file containing Cartesian
coordinates?
- Date: Tue, 10 Jan 2012 13:32:47 +0100
Sent to CCL by: "Tamas Gunda" [tgunda2[#]puma.unideb.hu]
Hi,
Mol2Mol has been made just for the input of files with unknown
formats. Any
kind of format can be inputted with it using the appropriate format
string.
Look at: www.gunda.hu/mol2mol
In this case copy the coordinates to the clipboard, open the file
input
window as general user input format,
and create and select the following input format string:
x y z d e d
(this is for x y z coodinates, dummy, element symbol, dummy)
and choose input from the clipboard
The data are inputted. The molecule looks quite odd as apart from two
OH
groups all of the z coordinates of carbon atoms are nearly zero.
Hope this helps
Tamas Gunda
--------------------------------------------------
From: "Andrew DeYoung andrewdaviddeyoung-
-gmail.com"
<owner-chemistry(0)ccl.net>
Sent: Sunday, January 08, 2012 20:50 PM
To: "Gunda, Gunda " <tgunda2(0)puma.unideb.hu>
Subject: CCL: What is the format of this file containing Cartesian
coordinates?
Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung*|*gmail.com]
Hi,
I have been reading the paper "Modeling of Graphite Oxide,"
Boukhvalov, D. W.; Katsnelson, M. I., J. Am. Chem. Soc. 2008, 130,
10697-10701. This paper has Supporting Information associated with
it, located here: http://pubs.acs.org/doi/suppl/10.1021/ja8021686 .
This Supporting Information contains the Cartesian coordinates for
various chemical species discussed in the paper (obtained by ab initio
calculations). For example, one of the series of coordinates that
this Supporting Information provides is the following:
-0.02689401 0.05432733 1.07516282 3 H 1
0.03282702 -0.01179385 0.68330051 2 O 2
0.60586594 -0.05478650 -1.06215854 3 H 3
0.54625340 0.01126245 -0.67028541 2 O 4
-0.00037430 0.00545262 0.11451905 1 C 5
-0.87007097 0.50375034 -0.04749619 1 C 6
-0.86607388 -0.50142967 -0.04692549 1 C 7
0.87536552 0.51049597 0.02025204 1 C 8
0.87795979 -0.51877321 0.02366501 1 C 9
-0.00283324 1.00386837 -0.01257709 1 C 10
0.00039748 -1.00136092 -0.01066833 1 C 11
-1.73307292 0.00197123 -0.03871588 1 C 12
-0.86683173 1.50543512 -0.02856670 1 C 13
-0.86909689 -1.50476823 -0.02691608 1 C 14
1.73809709 0.00167020 0.06437659 1 C 15
0.86891453 1.50286912 0.03907748 1 C 16
0.87181125 -1.50614862 0.04060303 1 C 17
-1.73625671 1.00707540 -0.04218536 1 C 18
-1.73743458 -1.00321958 -0.04099753 1 C 19
1.73948240 1.00519036 0.06254294 1 C 20
1.73748379 -1.00684011 0.06397068 1 C 21
-0.00097315 2.00519687 -0.00474136 1 C 22
-0.00025493 -2.00481803 -0.00256281 1 C 23
-2.60679486 0.50744858 -0.05730558 1 C 24
-2.60244033 -0.49997860 -0.05660149 1 C 25
-1.73600183 2.00826255 -0.03828653 1 C 26
-1.73589004 -2.00632024 -0.03581581 1 C 27
-0.86809971 2.50743539 -0.01969374 1 C 28
-0.86743107 -2.50800945 -0.01663035 1 C 29
1.73739025 -2.00803386 0.03602309 1 C 30
0.86918912 -2.50605556 0.01898868 1 C 31
-2.60674237 1.50998962 -0.06149746 1 C 32
-2.60337977 -1.50359739 -0.05952099 1 C 33
-0.00151756 3.01254125 0.00026303 1 C 34
-1.73833995 3.01353076 -0.04134158 1 C 35
1.73896850 -3.01089377 0.04144619 1 C 36
-2.60747482 2.51319434 -0.06379837 1 C 37
0.87160242 -3.51651549 0.01963025 1 C 38
-2.60959081 3.52137327 -0.06444686 1 C 39
1.74167046 -4.01903762 0.03732286 1 C 40
0.57935253 -0.00591929 -0.10150666 1 C 41
-0.29895259 0.51824224 -0.01065610 1 C 42
-0.29637000 -0.51095564 -0.00724144 1 C 43
-1.15911004 -0.00215128 -0.05137018 1 C 44
0.57861451 1.00085598 0.02367761 1 C 45
0.58190077 -1.00453933 0.02559150 1 C 46
-1.15848220 1.00634128 -0.05096692 1 C 47
-1.16048708 -1.00566650 -0.04953595 1 C 48
1.44505788 0.50095217 0.05994684 1 C 49
1.44905447 -0.50423433 0.06052232 1 C 50
-0.29287191 1.50575663 -0.02758935 1 C 51
-0.28990959 -1.50337425 -0.02606221 1 C 52
-2.02697593 0.50391544 -0.04217217 1 C 53
-2.02491349 -0.50419505 -0.04152028 1 C 54
1.44809109 1.50425324 0.03991273 1 C 55
1.44587383 -1.50598582 0.04156281 1 C 56
0.57921418 2.00435850 0.01557045 1 C 57
0.58001551 -2.00575731 0.01775155 1 C 58
-1.15838843 2.00756158 -0.02302302 1 C 59
-1.15757535 -2.00795444 -0.02057379 1 C 60
2.31207394 -0.00245438 0.05172946 1 C 61
-2.02776434 1.50719055 -0.04446594 1 C 62
-2.02602610 -1.50572182 -0.04269775 1 C 63
2.31642963 1.00271453 0.05400912 1 C 64
2.31524228 -1.00755964 0.05519446 1 C 65
-0.29021505 2.50557497 -0.00598370 1 C 66
-0.28747789 -2.51054533 -0.00287556 1 C 67
1.44708230 -2.50791413 0.03270193 1 C 68
2.31499473 -2.00876451 0.05130262 1 C 69
0.58051995 -3.01303700 0.01275161 1 C 70
-2.02771967 2.50972812 -0.04865231 1 C 71
-1.15998355 3.01040245 -0.02842868 1 C 72
2.31732484 -3.01400623 0.05435683 1 C 73
1.45151430 -3.51897104 0.03339008 1 C 74
-2.03208004 3.51717648 -0.04935652 1 C 75
2.31999134 -4.02068999 0.05257440 1 C 76
However, the Supporting Information (nor the article itself) appears
to specify the type of coordinate file that they are providing. For
example, is this in PDB format, XYZ format, or another format? Can
anyone please help me know which format this might be so that I can
save it in an appropriate file type and visualize the structure using
VMD?
Thank you kindly!
Andrew DeYoung
Carnegie Mellon University>