[gmx-users] [gmx-developers] Gromacs Project Query

Dallas Warren dallas.warren at monash.edu
Sun Feb 17 22:02:15 CET 2019

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a

On Sat, 16 Feb 2019 at 00:17, Matthew Atkinson <
matthew.atkinson-2 at student.manchester.ac.uk> wrote:

> Dear all,
> We are currently working on a project at the University of Manchester,
> which involves using GROMACS to understand the molecular dynamics of the
> biological machines for the walkers dynein and kinesin. However, when using
> the command *gmx_d pdb2gmx -f 5nvu_clean.pdb -o 5nvu_processed.gro -water
> spce *and selecting force field any force field 1-15, a resulting error
> “residue ‘UNK’ not found in residue topology” occurs. After searching and
> applying many solutions, a fatal error still occurs, what would you suggest
> we do? Would there be a force field not listed that we could use? The
> protein ID’s used are 5NVU and 3U06.
> Kind Regards,
> Matthew Atkinson
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