[gmx-users] md with multiple ligands

[Billy Williams-Noonan]

Well it depends how the OP has set up their simulation.   Was trying to
help.  :)  What you're saying is right of course.

On 2 July 2016 at 21:45, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/1/16 9:51 PM, Billy Williams-Noonan wrote:
>
>> Hi Justin,
>>
>> I've found that I get this error with my relative FEP calculations if my
>> .gro file with the relevant protein and ligand coordinates, describes the
>> protein numbering from a1-3017, and the ligand from 3018 onwards for
>> example, while in my topology file, a1-3017 refer to the same protein, and
>> afterwards I start label the first atom of my ligand as 1 again, instead
>> of
>> 3018.
>>
>> This problem usually pops up when I manually combine the relevant protein
>> and ligand molecule type and make an error with the numbering.
>>
>>
> Sure, in the case of merging [moleculetype] directives, all kinds of
> things change.  But for most normal simulations that do not require such
> operations, the ligand topology should be numbered from 1 (just as your
> merged [moleculetype] does, but that's a different case than what the OP is
> describing).
>
> -Justin
>
>
> Kind regards,
>>
>> Billy
>>
>> On Friday, 1 July 2016, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 6/30/16 11:22 PM, Billy Williams-Noonan wrote:
>>>
>>> Hi Thanh,
>>>>
>>>> Maybe try to check if the numbering of your atoms in the topology files
>>>> is
>>>> consistent with the .pdb or .gro files they describe.
>>>>
>>>>
>>>> Coordinate file and topology file numbering are different and use
>>> different conventions.  In fact, if one numbers a topology using global
>>> atom numbers from a coordinate file, it is what causes the error the OP
>>> reports.  Each [moleculetype] directive must be numbered consecutively
>>> from
>>> 1; after that, the only match with the coordinate file is based on the
>>> correct appearance of atom names (thus a link between [molecules] in the
>>> .top and the coordinates themselves).
>>>
>>> -Justin
>>>
>>> Billy
>>>
>>>>
>>>> On 1 July 2016 at 09:20, Thanh Le <thanh.q.le at sjsu.edu> wrote:
>>>>
>>>>
>>>> On Jun 30, 2016, at 3:48 PM, Thanh Le <thanh_le_quoc at yahoo.com> wrote:
>>>>>
>>>>>>
>>>>>> My name is Thanh Le, a graduate student in chemistry. Currently, I am
>>>>>>
>>>>>> using gromacs to do a dynamics simulation for my RNA-protein complex.
>>>>> I
>>>>> saw
>>>>> you posted a question titled “Atoms in the .top are not numbered
>>>>> consecutively from 1” on gromacs forum. I know it has been 3 years
>>>>> since
>>>>> you asked the question. I would like to know if you have solved the
>>>>> problem
>>>>> and how to fix this error?
>>>>>
>>>>> Hope to hear from you soon,
>>>>>> Thanks,
>>>>>> Thanh Le
>>>>>>
>>>>>>
>>>>> --
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>>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
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