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

Nuno Azoia nazoia at det.uminho.pt
Wed Nov 5 16:08:35 CET 2008 

On Wed, 2008-11-05 at 07:57 -0500, Justin A. Lemkul wrote:
> Please remember to keep all correspondence on the list for archiving purposes. 
> Also, others out there may have information to contribute.

Sorry about that. I just press Reply and I didn't check the e-mail
address.

I've solved the problem with your help.

I've tried what you have told me but I get the same error message.
Calling an .itp file within a .itp file always works with me (in version
3.3.1), but it makes more sense the way you describe, declaring
everything in the .top file.

The problem seems to be the posre.itp file itself. Even with the 3 files
I've told you (posre_A.itp, posre_B.itp and posre_C.itp), grompp needs a
posre.itp file. So the solution was to create a empty posre.itp file.
Now it's clear to me that my first option (see below the description of
the first posre.itp file I've created) makes no sense because by that
way I was calling each posre_*.itp file twice: once in the .top file and
the other in posre.itp file. Grommp was reading the posre.itp file
first, without any reference to any molecule, and it just don't work.

Thank you very much!

Nuno Azoia

> 
> Nuno Azoia wrote:
> > Hi Justin. Tank you for your answer!
> > 
> > Ok! I agree with you, and I'm doing something wrong. I just can
> > understand what. Can you please help me a little more.
> > 
> > In my .top file I have this lines
> > 
> > -----------------------------------------------------------
> > ; Include chain topologies
> > #include "krt_spd_C.itp"
> > #include "krt_spd_A.itp"
> > #include "krt_spd_B.itp
> > -----------------------------------------------------------
> > 
> > 
> 
> That should be fine.
> 
> > 
> > 
> > The krt_spd_C.itp is the topology of a peptide with 244 atoms.
> > krt_spd_A.itp and krt_spd_B.itp are peptides with 435 and 418 atoms,
> > respectively. In the last line of each .itp file I have something like
> > this (the letter changes with the corresponding file name)
> > 
> > -----------------------------------------------------------
> > ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre_A.itp"
> > #endif
> > -----------------------------------------------------------
> > 
> > 
> 
> This might be the problem.  You're calling an .itp file from within an .itp 
> file.  That may work, but I've never tried it.  Each .itp file should provide 
> the parameters for a single molecule, no more.  What I would try is the following:
> 
> ; Include chain topologies
> #include "krt_spd_C.itp"
> 
> #ifdef POSRES_C
> #include "posre_C.itp"
> #endif
> 
> #include "krt_spd_A.itp"
> 
> #ifdef POSRES_A
> #include "posre_A.itp"
> #endif
> 
> #include "krt_spd_B.itp"
> 
> #ifdef POSRES_B
> #include "posre_B.itp"
> #endif
> 
> That way, each chain topology is followed by its corresponding position 
> restraint file, under the appropriate [ molecule ] definition.
> 
> -Justin
> 
> > 
> > 
> > Each posre_*.itp file has positions restraints for all the atoms in the
> > peptide. For instance, posre_A.itp is something like this:
> > 
> > -----------------------------------------------------------
> > ; In this topology include file, you will find position restraint
> > ; entries for all the heavy atoms in your original pdb file.
> > ; This means that all the protons which were added by pdb2gmx are
> > ; not restrained.
> > 
> > [ position_restraints ]
> > ; atom  type      fx      fy      fz
> >      1     1  1000  1000  1000
> >      5     1  1000  1000  1000
> >      6     1  1000  1000  1000
> > (...)
> >    430     1  1000  1000  1000
> >    433     1  1000  1000  1000
> >    434     1  1000  1000  1000
> >    435     1  1000  1000  1000
> > ------------------------------------------------------------
> > 
> > 
> > 
> > 
> > Ok. In version 3.3.1 that's all I used to do. But now version 4.0
> > demands a posre.itp file, an so I've created this one, and at least by
> > this way grompp are reading my files
> > 
> > ------------------------------------------------------------
> > ; Include posre topology
> > #include "posre_A.itp"
> > #include "posre_B.itp"
> > #include "posre_C.itp"
> > ------------------------------------------------------------
> > 
> > 
> > 
> > 
> > That's why I can not understand what I'm doing wrong.
> > 
> > Another thing that I'm finding surprising is that, with two different
> > systems, in two different simulations, I get the same error in the 15th
> > position.
> > 
> > Thank you for your time.
> > 
> > Nuno Azoia
> > 
> > 
> > 
> > On Tue, 2008-11-04 at 13:14 -0500, Justin A. Lemkul wrote:
> >> 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
> >>> Fax: +351 253 510 293
> >>>
> >>> 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/
> >>
> >> ========================================
> > 
> > 
>

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