[gmx-users] Special atom distance matrix

[David van der Spoel]

On Mon, 2005-03-28 at 00:34 +0300, Dana Dogaru wrote:
> Hi,
> I have a question regarding how can one bind two new residues (which
> are not amino-acids).
> As far as I understood one has to write the new bonds in the
> specbond.dat file. If the distance between the two residues is within
> 10% of the distance given in specbond.dat file , then Gromacs will
> make a bond.
> Still , in the special atom distance matrix I have connected residues,
> which are far away.
I don't think so, unless you do it manually (with the -cys flag), but
that won't work for other stuff than disulphides I think.

-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++