[gmx-users] Ligand bond

[abelius]

It's a covalent bond. When I look at the .gro file before EM the bond is 
there, after EM it no longer is ...
Grompp Doesn't give any warnings.
 

David Mobley wrote:

> The "bond"? Is it covalently bound? If not, what do you mean? Do you 
> get any warnings when you run grompp?
>
> On 10/18/05, *abelius* < abelius at gmail.com <mailto:abelius at gmail.com>> 
> wrote:
>
>     Dear all,
>
>     I'm trying to run a simulation of a ligand bound to an enzyme. To
>     produce the *.itp I used the PRODRG server.
>     All goes well a first, but when I try to do an EM the bond between
>     enzyme and protein breaks.
>
>     Does anyone knows how I can fix this ?
>
>     thx in advance,
>
>     Abel
>
>
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