[gmx-users] Fwd: NO BONDS IN TOPOLOGY FILES

[Justin Lemkul]

On 8/31/15 4:03 AM, Alex Cullen wrote:
> Dear gmx-users,
>
> I am simulating a polymer, and I am really beginner in this area. when I
> execute pdb2gmx command I get posre.itp, topol.top, and conf.gro files, but
> there are no bonded, angles, and dihedral interactions in the topology
> file, only atoms and their chrges for each residue!

Then you haven't added any [bonds] in the .rtp file.  Without these, no bonded 
interactions can be generated.

-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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