[gmx-users] Problems with grompp and posre.itp in gromacs 4.0

[Justin A. Lemkul]

Quoting Nuno Azoia <nazoia at det.uminho.pt>:

> Hi!
>
> I'm having problems with grompp in version 4.0.
> When I attempt to run grompp I get this message. I've tried with two
> different systems, but the message is exactly the same
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0
> Source code file: toppush.c, line: 1196
>
> Fatal error:
> [ file posre_A.itp, line 16 ]:
> Atom index (15) in position_restraints out of bounds (1-14).
> This probably means that you have inserted topology section
> "position_restraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right
> molecule.
> -------------------------------------------------------
>
>
> I'm not understanding why is "Atom index (15)" out of bounds. The range
> (1-14), where did it came from?

grompp is finding a 15th atom to which it is trying to apply position
restraints, but it is unable to.

> It seems that I just can only have 14 position_restaints conditions, but
> this don't make any sense to me. Can anyone help with this? What do I
> have to do to solve this problem?
>

The error message is pretty clear - you have inserted #include "posre.itp"
within the incorrect molecule definition (i.e., it is in the wrong order or
wrong section in the .top).

-Justin

> Tank you
>
> Nuno Azoia
>
> --
>
> Nuno Gonçalo Azoia Lopes
>
> Laboratório de Investigação em Acabamento
> Departamento de Engenharia Textil
> Universidade do Minho
> Campus de Azurém
> 4800-058 Guimarães
> Portugal
>
> Tel: +351 253 510 280 - Ext: 517 289
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>
> Mobile: +351 965 382 487
> E-mail: nazoia at det.uminho.pt
>
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================