[gmx-users] top file definitions_1

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 6 22:58:37 CEST 2008

rosip at qb.ffyb.uba.ar wrote:
> Dear Community, 
> I am trying to manually define a .top file of an organic molecule (a 
> modified bisphosphonate). I am not a gromacs user but a lab mate is, so he
> will make the run. 
> It has been several days since I started to search for a text where the 
> .top format is depicted in detail but the only document I found was the one 
> of the UREA molecule.
> (http://www.gromacs.org/component/option,com_wrapper/Itemid,165/). 

Just for future reference - when posting links, open the frame in a new window 
and post that URL.  The one you post is the Search page, and not an actual post :)

> I need to have a detailed and didactic description of fields between [ ]
> and their columns of data 
> just to understand the example of the UREA. 

Try reading Chapter 5 of the manual.

> By the way, do you know whether there is a forum to share parameters of 
> molecules? 

Check the User Contributions section of the Gromacs site (within Downloads).


> Thank you very much, 
> Best regards, Pablo Rosi.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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