[gmx-users] Special atom distance matrix
feenstra at few.vu.nl
Thu Mar 31 08:36:26 CEST 2005
David van der Spoel wrote:
> On Mon, 2005-03-28 at 00:34 +0300, Dana Dogaru wrote:
>>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.
The matrix lists all distances, not only those that get connected.
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