[gmx-users] Fwd:question on salt bridges
spoel at xray.bmc.uu.se
Mon Oct 10 08:18:49 CEST 2005
On Mon, 2005-10-10 at 09:52 +0800, 孔韧 wrote:
> >From: Longzhu Shen <lzshen at emails.bjut.edu.cn>
> >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 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
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