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

[David]

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
atoms.

-- 
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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