[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
> 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:
>> 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.
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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