[gmx-users] md with multiple ligands

[Billy Williams-Noonan]

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.

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
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