[gmx-users] Is there any way to put dummy atoms into the n2t file of the CVS version of Gromacs?

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 4 08:44:39 CEST 2006

Arthur Roberts wrote:
> Hi, all,
>       I am interested in putting specific atom types
> into my n2t file in the CVS version of gromcas for use
> in x2top.  For example, in Gromacs 3.3.1, I used H2 to
> denote alkene proton and H3 to denote an alkyne
> proton.  However, in the CVS version of gromacs, I am
> not able to do that.  I would appreciate your input.
> Best wishes,
> Art
The atom type follows from the connections. I have considered 
implementing a more stricti mechanism, where you not specify the element 
to bind to but the atomtype. I presume this is mainly a problem for H 
for you now, isn't it?

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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