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

[Peter Kroon]

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...


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
>>>>>
>>>>> * 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.
>>>>>
>>>>
>>>
>>>
>>> -- 
>>> 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.
>>>
>>
>>
>