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

Alan alanwilter at gmail.com
Fri Oct 9 14:22:29 CEST 2015

Nicolas, if you have created your files in Amber, then the conversion to
GROMACS should be fine. You can find some details about it in


On 9 October 2015 at 12:39, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==================================================
> 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
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Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588

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