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

jalem...@vt.edu | (540) 231-3129


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