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

Arthur Roberts aroberts99163 at yahoo.com
Wed Oct 4 19:48:03 CEST 2006

Hi, David,

Yes, it is currently a problem for H.  However, it
might be important to do it, if you want to apply a
different force field on one side of the molecule than
another.  For example, let's say we have Lauric acid. 
A CH2 next to the carboxylate is going to have
different properties than one farther from the
carboxylate.  In NMR, CH2 near the carboxylate has
significantly different chemical shift and
T1-relaxation than one that is farther away from the
carboxylate.  It would also be nice to specify
different atom types without changing their effect on
the pdb file.  In other words, H2, which I specified
as an alkene proton, still works as a proton in most
molecular modeling packages.

Best wishes,

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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.
> 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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