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

[Mark Abraham]

On 17/01/2011 9:28 PM, Benjamin Bouvier wrote:
> 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).

The origin of the problem is probably there, but we'll need to see your 
topology.

> 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, 

Correct

> I checked that atoms 2 and 5 are indeed involved in an angle in the [ 
> agnles ] section... which they are...

OK, but we need the full information. The [bonds] section must have 2 
and 5 bonded to a common atom with a real bond type.

Mark