[gmx-users] Water molecule can not be settled‏

[Justin Lemkul]

On 7/4/16 5:43 AM, zeineb SI CHAIB wrote:
> Dear Mark,
>
> Thank you very much for your help.
>
> I checked the .itp file of my new parametrized molecule (THF) generated by pdb2gmx and it is not completed (only [atoms] entry, there is no [bonds], [angles] or [dihedrals] entries. Effectively, pdb2gmx failed to generate the topology of the THF.
>
> The thing that I can't understand is that in GROMACS manual they say that the entries [bonds],  [angles]...etc are optional when parametrizing a new molecule so I just added the [atoms] entry in the .rtp file and apparently it's not sufficient for GROMACS to generate the topology! Am I missing something?
>

Yes, you need [bonds] in order for pdb2gmx to do anything.  The only reason that 
a [bonds] directive is considered optional is because some species don't need it 
(ions, rigid water).  But you've got a molecule that requires bonds, so you need 
bonds.  pdb2gmx figures out the rest from the connectivity.

-Justin

-- 
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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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