[gmx-users] Fwd: Warning: 1-4 interaction

[Mark Abraham]

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.

Mark