[gmx-users] Fwd: Warning: 1-4 interaction
Mark.Abraham at anu.edu.au
Thu Apr 12 17:50:31 CEST 2007
Joern Lenz wrote:
> i know what this error message means. Their 1-4 distance is too long.
.... Their 1-4 distance *becomes* too long. It is likely this is because
of a topology problem that has nothing directly to do with the 1-4
interactions. Check the relevant region carefully.
> the mentioned atoms are of the DNA and the tyrosine respectively.
> my question now is: how can i fix this warning ? since i run minimzation and
> this warning occurs i do not know exactly how to go on becuase i run
> minimization in order to shrink the bond-length between protein and dna.
> how else can i shrink it to avoid the warning ?
If your topology is OK, you should use a starting structure close to the
geometry you're trying to build, possibly by using a minimization with
just a gentle harmonic restraint first of all, then building a new
topology with a bond when it's already close enough that you don't need
a large change to reach the minimum.
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