[AMBER] Possible bug on addLJType command of Parmed

From: Matias Machado <mmachado.pasteur.edu.uy>
Date: Sat, 28 Jul 2018 00:20:19 -0300 (UYT)

Dear Amber experts,

I found some issues while using the command addLJType of Parmed (AmberTools 16-18).

To exemplify the problem let assume a system with just 2 atom-types (named I and J in the force field) with the same LJ parameters.

When generating the topology, Leap will merge these two atom-types into a so called unique vdW-type "[1]".

The issues arise when executing the following commands in Parmed to edit the topology:

  addLJType .%I ;# This is OK, atom-type I is assigned to a new vdW-type "[2]", the problems come with the next commands...
  addLJType @%J ;# Because I and J already belong to different vdW-types ([1] and [2]), a new vdW-type "[3]" is created for a non-existing atom-type " "

  addLJType .%K ;# Also creates a new vdW-type "[4]" for a non-existing atom-type " "

In both cases a new vdW-type is created and linked to a ghost atom-type, which is impossible to edit or trace...

After saving the modified topology new LJ pointers as well as A and B coefficients are written to the file, however they remain as "orphan parameters" in the topology...

I don't know if this is a harmless bug or it does affect the simulation, but the desired behavior for addLJType would be do nothing if the mask points to a non-existing atom-type or if the selection in the mask is irreducible.

That would be particularly helpful for applying general fixes/modifications to LJ parameters of any topology without the need to be sure about the presence of all the involved atom-types



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

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Received on Fri Jul 27 2018 - 20:30:03 PDT
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