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

Berk Hess gmx3 at hotmail.com
Wed Nov 5 16:28:27 CET 2008 

Hi,

I just ran the 4.0 version of pdb2gmx on a multi-chain pdb file
and posre.itp does not appear anywhere.

>From the file names it seems that the files are non-standard
and made of modified by hand.
So maybe you somehow modified a file with posre.itp in it?

Berk


> Date: Wed, 5 Nov 2008 10:11:03 -0500
> From: jalemkul at vt.edu
> To: nazoia at det.uminho.pt; gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0
> CC: 
> 
> 
> 
> Nuno Azoia wrote:
> > 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.
> > 
> 
> Well, I'm glad it worked, but having to create an empty posre.itp file sounds a 
> bit nonsensical to me.  Maybe the developers can help us out - has something 
> within grompp changed that makes a posre.itp file explicitly necessary?
> 
> -Justin
> 
> > 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
> >>>>>
> >>>>> _______________________________________________
> >>>>> gmx-users mailing list    gmx-users at gromacs.org
> >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>>>> Please search the archive at http://www.gromacs.org/search before posting!
> >>>>> Please don't post (un)subscribe requests to the list. Use the
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> >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>>>
> >>>>
> >>>> ========================================
> >>>>
> >>>> 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/
> >>>>
> >>>> ========================================
> >>>
> > 
> > 
> 
> -- 
> ========================================
> 
> 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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