[gmx-users] Re: gmx-users Digest, Vol 61, Issue 31

Alan alanwilter at gmail.com
Fri May 8 18:51:14 CEST 2009

Yes, 4.0.4.

I know topolbuild well, but I've been working on application (acpypi)
that is essentially python interface for antechamber with "steroids"
and able to generate topol files for GMX with AMBER99SB/GAFF

I've doing some tests with the possibility of generating OPLS/AA as
well. I was just trying to find other topol gen tools to compare.

I proper announcement will come soon.


On Fri, May 8, 2009 at 14:53,  <gmx-users-request at gromacs.org> wrote:
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> 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
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

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