[gmx-users] x2top taking too long

David van der Spoel spoel at xray.bmc.uu.se
Fri May 8 15:18:38 CEST 2009

Justin A. Lemkul wrote:
> Is this version 4.0.4?  I get the same thing under the newest version.  
> I think x2top fluctuates in terms of its level of usability, since it is 
> in an ongoing state of development.  Older versions (i.e., 3.3.3) should 
> work, at least in terms of generating a basic topology.

There are a number of user contributions for this purpose on the website 
(topolbuild, mktop), please check them out. A real improvement will come 
with version 5.0

> -Justin
> Alan wrote:
>> Hi there,
>> So I decided to give a try with x2top.
>> x2top -f aaa.gro -o aaa.top
>> However, the program starts and seems to never finishing holding as:
>> [snip]
>> There are 23 name to type translations
>> Generating bonds from distances...
>> atom 0
>> And 'atom 0' stays there while I clearly see my cpu running with x2top.
>> Mac intel with GMX via Fink.
>> Many thanks in advance.
>> Alan

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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