[gmx-users] Fwd:question on salt bridges

[David]

On Mon, 2005-10-10 at 09:52 +0800, 孔韧 wrote:
> >From: Longzhu Shen <lzshen at emails.bjut.edu.cn>
> >Reply-To: 
> >To: kongren at emails.bjut.edu.cn
> >Subject: question on salt bridges
> >Date:Sun, 9 Oct 2005 11:53:52 -0400
> >
> >Dear Sir/Madam,
> > 
> > I am using the command g_saltbr to inverstigate the salt bridges based on the 
> > trajactory produced by gromacs v3.2.1 program. Out of my expectation, I 
> > frequently found pairs between charged residues and non-charged residues, 
> > like  GLU   63  VAL  180 , LYSH  146 -- LEU  188 in the file of plus-min.xvg. 
> > This really made me a bit confused about the defination on the salt bridge in 
> > gromacs. I am wondering whether any experienced users could give me a proper 
> > explanantion. Your kindness would be highly appreciated. 
> > 

You can throw them out of the output if you don't want the information,
but it should be possible to select only true salt bridges.

> > sincerely,
> > 
> > Longzhu Shen
> >
> 
> 
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-- 
David.
________________________________________________________________________
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://xray.bmc.uu.se/~spoel
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