[gmx-users] Topology and co-ordinates do not match

Natalie Tatum nataliejtatum at gmail.com
Wed Sep 20 14:47:19 CEST 2017


Hi Justin and Peter,

I had a previous warning for the [ defaults ] present in the ligand
topology, but none for the other duplicate sections. I'd removed the [
defaults ] but with no further information on the error besides the
topology/co-ordinate mismatch, I had no idea where to go.

Thanks for the tip, I'll definitely keep an eye out on future outputs!

Natalie

On 20 September 2017 at 13:27, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/20/17 8:24 AM, Peter Kroon wrote:
>
>> I was kind of surprised to see a top could contain multiple [system] and
>> [molecules] sections. Is this intentional? I can't come up with a
>> use-case...
>>
> Indeed, that should have failed with an error, and I also can't figure out
> why it worked.
>
> -Justin
>
>
>
>> Peter
>>
>>
>> On 20-09-17 14:15, Justin Lemkul wrote:
>>
>>>
>>> On 9/20/17 8:13 AM, Natalie Tatum wrote:
>>>
>>>> Hi Peter,
>>>>
>>>> Deleting this lines appears to have worked and I've progressed
>>>> through to
>>>> minimising the complex. THANK YOU. I don't think I would ever have
>>>> spotted
>>>> that on my own!
>>>>
>>> A tip when generating ligand topologies (since many programs generate
>>> them as if they were their own system): a .top should describe a full
>>> system and a .itp should describe a molecule (and its parameters, if
>>> necessary).  As a rule of thumb, you should *never* see the following
>>> in an .itp:
>>>
>>> 1. A [defaults] directive (or an #include statement to a parent force
>>> field that will have one)
>>> 2. A [system] directive
>>> 3. A [molecules] directive
>>>
>>> This is the primary difference between the two.
>>>
>>> -Justin
>>>
>>> Natalie
>>>>
>>>> On 20 September 2017 at 12:54, Peter Kroon <p.c.kroon at rug.nl> wrote:
>>>>
>>>> Hi Natalie,
>>>>>
>>>>>
>>>>> I think the problem is your GMX_DRG.itp defines a [system] and
>>>>> [molecules] section containing a DRG molecule at the bottom.
>>>>>
>>>>>
>>>>> Peter
>>>>>
>>>>>
>>>>> On 20-09-17 13:45, Natalie Tatum wrote:
>>>>>
>>>>>> Hi Peter,
>>>>>>
>>>>>> Yes. The protein is 4600 atoms, I edited to 4647 to account for the
>>>>>>
>>>>> ligand
>>>>>
>>>>>> of 47 atoms at the end of the gro file. The ligand is carried through
>>>>>>
>>>>> into
>>>>>
>>>>>> the subsequent co-ordinate files, but as soon as I hit grompp I
>>>>>> have an
>>>>>> issue.
>>>>>>
>>>>>> Natalie
>>>>>>
>>>>>> On 20 September 2017 at 12:42, Peter Kroon <p.c.kroon at rug.nl> wrote:
>>>>>>
>>>>>> Hi Natalie,
>>>>>>>
>>>>>>>
>>>>>>> did you change the particle count on the second line of your gro
>>>>>>> file?
>>>>>>>
>>>>>>>
>>>>>>> Peter
>>>>>>>
>>>>>>>
>>>>>>> On 20-09-17 13:31, Natalie Tatum wrote:
>>>>>>>
>>>>>>>> Dear all,
>>>>>>>>
>>>>>>>> I have what appears to be a common problem but I can't seem to track
>>>>>>>>
>>>>>>> down
>>>>>
>>>>>> the solution. The number of coordinates in my coordinate file
>>>>>>>> (complex_solvated.gro, 73587, does not match topology (topol.top,
>>>>>>>>
>>>>>>> 73634).
>>>>>
>>>>>> This is of course a difference of 47 atoms, the precise number in my
>>>>>>>>
>>>>>>> ligand.
>>>>>>>
>>>>>>>> As far as I can tell, I have correctly appended my ligand.gro to my
>>>>>>>> complex.gro, changing the corresponding header +47, and this is
>>>>>>>> carried
>>>>>>>> through to complex_solvated.gro. The numbers at the bottom of
>>>>>>>> topol.top
>>>>>>>>
>>>>>>> sum
>>>>>>>
>>>>>>>> to match the co-ordinate file (22980*3 + 4600+47).
>>>>>>>>
>>>>>>>> So, I'm honestly not sure how this error is (a) coming about and (b)
>>>>>>>>
>>>>>>> can
>>>>>
>>>>>> be
>>>>>>>
>>>>>>>> solved. I'm thinking perhaps the topology isn't correctly
>>>>>>>> including the
>>>>>>>> ligand topology, but I have placed that in the topol.top
>>>>>>>> correctly as
>>>>>>>>
>>>>>>> far
>>>>>
>>>>>> as I can see. The ligand topology was created in Antechamber and
>>>>>>>>
>>>>>>> converted
>>>>>>>
>>>>>>>> with ACPYPE.
>>>>>>>>
>>>>>>>> Relevant files are here:
>>>>>>>>
>>>>>>>> complex.gro: https://drive.google.com/open?id=0B8FqO1m_a-
>>>>>>>>
>>>>>>> iGSXVYTW5qQk1rSUE
>>>>>>>
>>>>>>>> complex_solvated.gro:
>>>>>>>> https://drive.google.com/open?id=0B8FqO1m_a-iGem02WGlQWWlDS0U
>>>>>>>>
>>>>>>>> DRG_GMX.gro: https://drive.google.com/open?id=0B8FqO1m_a-
>>>>>>>>
>>>>>>> iGUVZ3eFZieEtiRUE
>>>>>>>
>>>>>>>> DRG_GMX.itp: https://drive.google.com/open?id=0B8FqO1m_a-
>>>>>>>>
>>>>>>> iGS19wSVAySlhaTVk
>>>>>>>
>>>>>>>> topol.top: https://drive.google.com/open?id=0B8FqO1m_a-
>>>>>>>>
>>>>>>> iGSWlQMnhSUm15b3c
>>>>>
>>>>>> Can anyone shed light on where I'm going wrong?
>>>>>>>>
>>>>>>>> Much appreciated,
>>>>>>>>
>>>>>>>> Natalie
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ----
>>>>>>>>
>>>>>>>> Dr. Natalie J. Tatum
>>>>>>>> PDRA | NICR, Newcastle University
>>>>>>>>
>>>>>>> --
>>>>>>> Gromacs Users mailing list
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>>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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-- 
*Dr. Natalie J. Tatum*
Post-doctoral Research Associate
Northern Institute for Cancer Research
Newcastle University


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