[gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype)

Justin Lemkul jalemkul at vt.edu
Fri Oct 9 13:41:16 CEST 2015

On 10/8/15 11:48 AM, Nicolas Cheron wrote:
> Dear all,
> I am joining a project where people are using the CHARMM22 force field.
> They converted a .prmtop file from Amber to Gromacs format with acpype. In
> the output topology, there are no Urey-Bradley potentials or improper
> dihedrals (for example, all the [ angle ] functions are of type 1 and none
> are 5 and all the [ dihedrals ] function are of type 9 and none are 2).
> I am confused, and I am wondering if something went missing when using
> acpype? Do you know how acpype handle this part of the amber topology? Or
> did acpype converted the Urey-Bradley and improper dihedrals from the
> .prmtop to other kind of functions? For an angle A-B-C with Urey-Bradley, I
> thought it would be possible to have a force as if there was a bond between
> A and C but I didn't find anything like that in the topology.
> The manual says about Urey-Bradley potential "Although this can be easily
> written as a simple sum of two terms, it is convenient to have it as a
> single entry in the topology file and in the output as a separate energy
> term" but I am not sure to understand if that means that Gromacs developers
> have prefered to keep it as a single entry or not.

Yes, it is a single entry.

Not all U-B angles in CHARMM have an explicit 1-3 term, but if the conversion is 
simply nixing those that exist, clearly the conversion is being done wrong.  If 
impropers are present yet disappearing, this is more evidence that the program 
is not designed to do what you want it to, or that there is some problem with 
the input itself.

The simplest test is to do a single-point energy in AMBER and GROMACS and 
compare the outcome to determine if the newly generated topology is sensible. 
If there's a mismatch, find a better method of conversion.



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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