[gmx-users] Re: gmx-users digest, Vol 1 #506 - 6 msgs

[Luke Czapla]

Hi David,

  Aren't the tdb files specific to proteins?  I can't use them because of
the point that they are -c and -n for C and N terminii.  I'm talking about
the 5' phosphate group and the 3' hydroxyl group.  I don't see any kind of
syntax you could use in a tdb file, but if you have any idea, let me know,
because I know which atoms to remove/add, but not the basic concept of
using a tdb file for DNA or RNA.

thank you,
Luke

> 
> Message: 5
> Subject: Re: [gmx-users] question about DNA simulation 5'&3' ends
> From: David <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Date: 30 Nov 2002 00:22:07 +0100
> Reply-To: gmx-users at gromacs.org
> 
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>