[gmx-users] error while running gmx grompp

[Elton Carvalho]

Hello, Dinesh,

Please direct your questions to the GROMACS user list, I'm unfortunately
not always able to respond to individual questions and the list has its
share of experts that can respond in a timely manner.

In your case I would check if the dihedrals defined in line 37 of file
mmb.prm are already defined somewhere else in any topology files alerady
#include'd.

Example: ffbonded.itp has a [ dihedraltypes ] line with atoms 4 5 7 8, then
you #include mmb.prm and it also has atoms 4 5 7 8 in a [ dihedraltypes ]
block. This is unsupported because if the dihedral type  is 9, it means
that these parameters should be added, but the lines defining this dihedral
are not consecutive, meaning that it's likely that you are trying to
redefine the dihedral. Since this is ambiguous and some sort of borderline
case, thye devs decided to issue a warning that this behavior is
unsupported.

This warning message is the result of a bug [
https://redmine.gromacs.org/issues/2077 ] I reported because of this
ambiguity. Please read the redmine issue to better understand what happened.

To solve your issue, look at like 37 of your mmb.prm and check if the 4
atoms defined in that dihedral are present somewhere else in your
#include'd files.

Cheers from a cloudy, humid and hot Natal,

On Wed, Feb 20, 2019 at 2:52 AM Nath, Dinesh <Dinesh.Nath-1 at ou.edu> wrote:

> Hi Elton
>
>
>
> I cam across your message on gromacs mail archive and it seems I am stuck
> with similar problem as you mentioned in following message:
>
>
>
> My apologies,
>
>
>
> After careful inspection, I noticed that I had #included a copy of
>
> this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [
>
> dihedraltypes ] directive is actually loaded twice, hence the
>
> warnings. Removing the #include from forcefield.itp and keeping it in
>
> the .top file eliminated the warnings and the resulting dynamics seems
>
> sane (read: did not explode).
>
>
>
> Lesson learned: don't change the standard forcefield definition files
>
> when doing preliminary testing. Especially in the end of a 12h layover
>
> between flights.
>
>
>
> Thank you for your attention,
>
> --
>
> Elton
>
>
>
> Here is the error message which I am receiving. I am sending you my
> topol.top file. I will really appreciate if you could suggest what I am
> doing wrong. Because I am not clear about what changes to make in topol.top
> file to avoid the following error:
>
>
>
>
>
> ERROR 1 [file mmb.prm, line 37]:
>
>   Encountered a second block of parameters for dihedral type 9 for the same
>
>   atoms, with either different parameters and/or the first block has
>
>   multiple lines. This is not supported.
>
>
>
> Looking forward to your response.
>
>
>
> Thank you in advance.
>
>
>
> Kind regards
>
>
>
>
>
> __________________________________
>
> Dinesh Nath, Ph.D.
>
> The University of Oklahoma
>
> Postdoctoral Research Fellow
>
> Department of Chemistry & Biochemistry
>
> Institute for Natural Products Applications
>
> & Research Technologies (INPART)
>
> 101 Stephenson Parkway
>
> Norman, OK 73019
>
> (412) 908-3476
>
> dinesh.nath-1 at ou.edu
>
>
>
>
>


-- 
Elton Carvalho