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

Nicolas Cheron nicolas.cheron.boulot at gmail.com
Thu Oct 8 17:49:32 CEST 2015

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.

Thanks for your help


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