[gmx-users] Residue modifications

David spoel at xray.bmc.uu.se
Wed Jun 25 09:22:01 CEST 2003

On Tue, 2003-06-24 at 18:31, Anu Tervo wrote:
> Hi all,
> I'd like to get some advice for my task in hand. I need to remove HG atom
> from one Ser residue in my protein to get a free OG atom. What would be
> the best way to do this: just delete the corresponding atom from .top and
> manually edit atom numbers to match again, create an .rtp file for Ser 
> - HG residue, or define HG as a dummy atom (in this case, what dummy would
> be the best for this usage)? 
you want to make a new rtp entry, take the current ser one, copy it to
e.g. SEQ and modify it (don't forget to create a corresponding hdb entry
> Ciao,
>     -Anu
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel

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