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, Art --- David van der Spoel <[EMAIL PROTECTED]> 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 > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
