From owner-chemistry@ccl.net Wed Jan 11 08:25:00 2012
From: "Tamas Gunda tgunda2!^!puma.unideb.hu" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL: What is the format of this file containing Cartesian coordinates?
Message-Id: <-46141-120110073257-7640-2Z2evf40bvRHciCvbCNepA*|*server.ccl.net>
X-Original-From: "Tamas Gunda" <tgunda2---puma.unideb.hu>
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Date: Tue, 10 Jan 2012 13:32:47 +0100
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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>
>