[gmx-users] Missing bond

Justin Lemkul jalemkul at vt.edu
Mon Apr 3 13:50:16 CEST 2017

On 4/1/17 1:18 AM, Sudip Das wrote:
> Dear All,
> While I am preparing my system topology with pdb2gmx for a system
> containing enzyme with 30 non-ionic surfactant molecules in water, I got 36
> number of bonds per surfactant molecules, but actually it has 37 bonds
> (anyways, the number of angle, dihedral etc. are correct). From the
> generated topology for this surfactant, I found out the missing bond. But I
> checked that I have incorporated that bond in aminoacids.rtp file and that
> bond type is also present in the ffbonded.itp file.
> To figure out the reason, I used the pdb2gmx for a system with only 30
> surfactant molecules in water (no enzyme). Again I encountered the same
> problem.
> So, what could be the solution? Please assist me.

Something does not add up.  Angles and dihedrals are built from the bonds, so if 
there's a bond missing, the angles and dihedrals shouldn't be right.  Which bond 
is missing?  If it's in the .rtp there's no way it is somehow ignored while the 
others get processed correctly.



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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