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

Wed Nov 5 17:07:45 CET 2008

Hi,

I just ran grompp and it does not complain about anything (and no posre.itp file).

Are you really sure there is no reference to posre.itp in your files?
Try:
grep posre *.itp *.top

Berk

> Subject: RE: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0
> From: nazoia at det.uminho.pt
> To: gmx-users at gromacs.org
> Date: Wed, 5 Nov 2008 15:53:16 +0000
> 
> On Wed, 2008-11-05 at 16:28 +0100, Berk Hess wrote:
> > Hi,
> > 
> > I just ran the 4.0 version of pdb2gmx on a multi-chain pdb file
> > and posre.itp does not appear anywhere.
> 
> When I've run pdb2gmx on my multi-chain pdb file I get posre_*.itp files
> automatically because in my pdb file I have chain identifiers; I have
> chain A and chain B, and Gromacs assumed chain C. That files was not
> "hand made".
> 
> Now I've tried to run pdb2gmx on the same pdb file, but without chain
> identifiers and I get just one posre.itp file with all the information.
> 
> But the real question is not that. Why is grompp asking for a posre.itp
> file that's not declared anywhere? In the .top file I declared my
> posre_*.itp files, so why is grompp ask me for posre.itp? And the
> strange thing is that with a empty file everything is working now.
> 
> Have you tried to run energy minimization on multi-chain system, having
> no posre.itp file?
> 
> Nuno Azoia
> 
> > 
> > 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
> > > >>>>>
> > > >>>>> ï»¿--
> > > >>>>>
> > > >>>>> Nuno GonÃ§alo Azoia Lopes
> > > >>>>>
> > > >>>>> LaboratÃ³rio de InvestigaÃ§Ã£o em Acabamento
> > > >>>>> Departamento de Engenharia Textil
> > > >>>>> Universidade do Minho
> > > >>>>> Campus de AzurÃ©m
> > > >>>>> 4800-058 GuimarÃ£es
> > > >>>>> 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
> > > >>>>> www interface or send it to gmx-users-request at gromacs.org.
> > > >>>>> 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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