[gmx-users] md with multiple ligands

[Justin Lemkul]

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

==================================================