[gmx-users] Grompp errors while changing combination rules

[Justin Lemkul]

On 7/17/18 5:40 AM, Apramita Chand wrote:
> Dear All,
> I had enquired earlier about the steps for changing combination rules in
> GROMOS ff. As I understood from your answers, if I am to take combination
> rule 3, I can put  sigma and epsilon for my atomtypes under the C6 and C12
> columns in ffnonbonded.itp  and these numbers will be interpreted as sigma
> and epsilon when I specify the combination number. Also, I don't need to
> add anything in the non-bonded params section as  the interactions will be
> automatically calculated. I have specified the 'gen-pairs'=yes in the

The gen-pairs keyword has no real relation to the combination rule, it's 
there to do what it says: generate 1-4 pair parameters when not present 
in ffnonbonded.itp.

> defaults section for this purpose. But when I try to minimise the system I
> get the message:
>
> Too many warnings (2862), g_grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
>
>
> WARNING 2862 [file ffnonbonded_modified.itp, line 2927]:
>    Too few parameters on line (source file
>    /builddir/build/BUILD/gromacs-4.5.7/src/kernel/toppush.c, line 820)

Any reason you are using wildly outdated (and unsupported) software?

>
>
> I had taken the exact same system and files with combination rule 1 and the
> simulation ran smoothly.
>
> What could be the problem? Is there anything I have missed out ?Should I
> use the maxwarn option?

Absolutely not. "Too few parameters on line" means the format of what 
you have provided grompp is not correct. Your model physics will not be 
realistic, if the resulting simulation even runs.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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