[gmx-users] md with multiple ligands

[Justin Lemkul]

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

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