[gmx-users] question about DNA simulation 5'&3' ends

David spoel at xray.bmc.uu.se
Sat Nov 30 00:22:07 CET 2002

On Sat, 2002-11-30 at 00:32, Luke Czapla wrote:
> Hi all,
>   I want to remove the 5' Phosphate from the 5' end and add a hydrogen to
> the O3* of the 3' end of a 10bp oligonucleotide double stranded helix.  I
> was wondering if I had to add this explicitly in the rtp (by making new
> residues) or if there was something similar to the N and C terminii
> database for this type of thing.  The only other resort I have is to
> modify the pdb2gmx source code some more.
Can't you do it with the .tdb files? You can remove, add and replace

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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