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
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