Pair Interaction calculation of PDB with lone pairs.

[HanatoK]

If I run a pair interaction of a PDB structure with lone pairs, NAMD 2.14 will crash with the following error:

FATAL ERROR: Low global exclusion count!  (19976 vs 19978)  System unstable or pairlistdist or cutoff too small.

This happens on NAMD 2.14 and NAMD 3. NAMD 2.11 does not have this regression.

Current workaround: Add ignoreMass on to the NAMD configuration file.

[ReneHamburger1993]

I just had the same issue with NAMD 2.14 Analyzing the interaction of a molecule's charge group versus the rest of the system.

• 1st case:
  • Group1: charge group of a ligand. Group2: everything except the ligand -> worked
• 2nd case:
  • Group1: charge group of ligand. Group2: rest of the ligand and everything else -> did not work.

2nd case worked including the workaround from above ignoreMass on Can I still be sure the 1-4 interactions are excluded properly?

[HanatoK]

I just had the same issue with NAMD 2.14 Analyzing the interaction of a molecule's charge group versus the rest of the system.

* 1st case:

  * Group1: charge group of a ligand. Group2: everything except the ligand -> worked

* 2nd case:

  * Group1: charge group of ligand. Group2: rest of the ligand and everything else -> did not work.

2nd case worked including the workaround from above ignoreMass on Can I still be sure the 1-4 interactions are excluded?

Sorry, I am not sure. I only tried my workaround with PDB files with lone pairs. In general, I use pair interaction between two molecules, which is not your case (charged group vs others in the same molecule).

[ReneHamburger1993]

I checked the NAMD source code and the keyword ignoreMass is used to prevent detection of hydrogens and others by mass. Though this should not effect any of the remaining calculations. Thanks René