[gmx-users] Problem with GB and coarse-grain forcefield

Benjamin Bouvier benjamin.bouvier at ibcp.fr
Mon Jan 17 11:28:23 CET 2011

Hi all,

I'm trying to simulate a coarse-grained system using a custom force field,  
and the GB algorithm to account for solvent. I generate the relevant ITP  
and TOP files using my own code (including an [ implicit_genborn_params ]  
section containing the Born radii).

When GB is disabled, grompp and mdrun run fine. When I activate GB however  
(implicit_solvent =  GBSA, gb_algorithm =  HCT), grompp throws an error:
Program grompp, VERSION 4.5.3
Source code file: topio.c, line: 465

Fatal error:
Cannot find length for atoms 1-4 involved in angle
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Before crashing grompp correctly processes 'angles' 0-2, 0-5 and 1-3  
(checked using gdb). Assuming these refer to 0-based atom serial numbers,  
I checked that atoms 2 and 5 are indeed involved in an angle in the [  
agnles ] section... which they are...

I'd appreciate any pointer as to what I'm missing here... Thanks in  


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