[gmx-users] Potential issue using acpype to convert amber topology to gromacs

Justin Lemkul jalemkul at vt.edu
Wed Feb 14 15:43:46 CET 2018

On 2/14/18 9:42 AM, Justin Lemkul wrote:
> On 2/14/18 9:33 AM, Easton J.W. wrote:
>> Thanks Justin,
>> Will this effect the interactions (both bonded and non-bonded) that 
>> these atoms have, as their atom types are not in the forcefield itp 
>> files?
> Missing atom types would cause grompp to fail; you'd never get to the 
> point where a simulation would be affected.
> You're introducing custom atom types in the topology itself, and 
> that's always legal before any [moleculetype] appears. The LJ 
> parameters come from the [atomtypes] directive. Masses and charges 
> present in that directive aren't used.

Actually, to clarify: *if* masses are present in the [atoms] directive 
of a [moleculetype], then the masses found in [atomtypes] are not used. 
Strictly speaking, it is not necessary to have explicit masses in 
[atoms], though nearly all topologies do.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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