[gmx-users] Re: converting pdb to gmx successfully

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 7 22:06:03 CET 2006

David Mathog wrote:
> Can anybody tell my why DT, DT5, DT3 and DTN use "O" instead of "O2"
> in the Amber rtp file?  The other O in the base is labeled "O4" and
> it just seems strange and somewhat illogical that O2 would not be
> given an analogous name.
Not sure but it could be because gromacs filters out atoms with names 
like O2 and O1 (which are usually in the C-terminus of a protein).

> Thanks,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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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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