[gmx-users] x2top finds 10+ bonds on atoms

[paul buscemi]

Found the problem, 

In using the -ff select option,  x2top was being directed to an incorrect  gromos54a7 .ff directory - not the one in the local directory - with an incorrect n2t.  x2top was apparently doing its best to make something.

> On Feb 7, 2019, at 7:07 PM, paul buscemi <pbuscemi at q.com> wrote:
> 
> Dear gmx users,
> 
> I’ve been using x2top for some time with success..  I recently taken a polymer whose itp was created with x2top and using the same 55a7 ff and re-ran it as a demo-tutorial. 
> 
> In leaning how to use x2to and atomname2type I expected  the error “ Cannot find forcefield for atom x”  This time I have many such errors on this previously rune molecule as “Can not find force field  for atom C 4444 with bonds or atom N555 with 37 bonds.  The pdb  and gro files open just fine with VMD and Avogadro.
> 
> Any hints what might cause such weird outcome ?  There is no log file to include, and the pdb text looks normal - has the name “HETATM”  in the first column
> 
> 
> Gromac 18.3  Linxux mint  Mat 20.1
> 
> 
> thanks
> Paul
> 
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