From: Roman Shirokov (
Date: Tue Sep 03 2013 - 16:44:57 CDT


I've encountered the same problem while doing SWM4-NP and polarizable ions in NAMD2.9.
A similar problem with NAMD2.9 was reported previously in another post ("five 'ERROR' in the log file of NAMD2.9" from May 13, 2012).
As it is discussed in that post, there is only one place in the source code that gives such a message, it is in molecule.c:

line 2429: if ( (atoms[i].mass<1.5) != (lcpoParamType[i]==0) ) {

If one has atoms with mass <1.5 and their type is not "H", the not telling much string 'ERROR' is sent to the output.

This is clearly a nuisance bug that came with using LCPO in NAMD2.9.
The check is done regardless of whether or not GBIS/SASA/LCPO calculation is performed.

When a polarizable FF is implemented, DRUDE particles and lone pairs with mass <1.5 can be numerous.
For each of them the output gets unrelated but scary "ERROR" message.

I hope it gets clarified in the next version.

Roman Shirokov
Department of Pharmacology & Physiology
NJMS - Rutgers Biomedical and Health Sciences

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:36 CST