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

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 5 16:11:03 CET 2008 


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
>>>>>
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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/
>>>>
>>>> ========================================
>>>
> 
> 

-- 
========================================

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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