[gmx-users] No bond information

[Anton Feenstra]

Dmitry Kovalsky wrote:
> 
> Hi there
> I'm trying to set up MD with shake
> but when I started grompp I got:
> 
> Generated 135 of the 1081 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> turning all bonds and angles into constraints...
> Cleaning up temporary file gromppnI82Iu
> Fatal error: No bond information for bond H1-N or N-H2
> 
> part of mdp file is
> constraints    = all-angles
> constraint_algorithm  = shake
> 
> but when I try
> constraints    = all-bonds
> everything is ok!
> I know that shake does work with angles
> What is the problem?

AFAIK all-angles constraints are not supported in the current
forcefields.
Additionally, for a protein it has been shown (there is a reference but
I don't have it here) that this leads to a un-naturally rigid protein.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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