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

[Justin Lemkul]

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
>>>>>> -- 
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>>>>
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>>>
>
>
>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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