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

[Justin Lemkul]

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

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
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