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

[Peter Kroon]

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
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>