[gmx-users] No bond information

Dmitry Kovalsky dikov at imbg.org.ua
Sat Jun 29 11:12:19 CEST 2002

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?

Sincerely yours,


Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143

E-mail: dikov at imbg.org.ua
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589

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