[gmx-users] error in equilibration

[Mark Abraham]

On 9/02/2011 11:07 PM, shiva birgani wrote:
> Dear Justin
> I fallowed your tutorial of "Protein-Ligand Complex" to simulate a 
> peptide associated with acetic acid. All the step was good but in 
> Equilibration phase 1 I encountered with this error
>
> WARNING 1 [file nvt.mdp, line unknown]:
>   Unknown left-hand 'continuation' in parameter file
>
> checking input for internal consistency...
> calling cpp...
> processing topology...
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> turning all bonds into constraints...
> Excluding 3 bonded neighbours for ACY 1
> turning all bonds into constraints...
> Excluding 2 bonded neighbours for SOL 6648
> turning all bonds into constraints...
> Excluding 1 bonded neighbours for NA+ 1
> turning all bonds into constraints...
> Excluding 1 bonded neighbours for CL- 0
> turning all bonds into constraints...
> NOTE:
>   System has non-zero total charge: -9.999999e-01
>
> processing coordinates...
> double-checking input for internal consistency...
> WARNING 2 [file "topol.top", line 1453]:
>   For energy conservation with LINCS, lincs_iter should be 2 or larger.
>   You can safely ignore this if your system doesn't have any
>   LINCS-constrained bonds;
>   for water molecules we normally use the analytical SETTLE algorithm
>   instead.
> Setting gen_seed to 261405
> Velocities were taken from a Maxwell distribution at 300 K
>
> There were 2 warnings
>
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: grompp.c, line: 1132
>
> Fatal error:
> There were 1 error(s) processing your input
> -------------------------------------------------------
>
> how should I do correct it?

You're probably using a version of GROMACS that is years older than the 
tutorial, and so will have minor compatibility issues. More recent 
versions offer much better performance.

Mark
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