Setting up symmetry restraints in a homo-dimer with non-equal number of residues

From: Mark Hilge (
Date: Fri Dec 09 2016 - 00:17:19 CST

Dear namd users,

I am using namd via the xMDFF module to refine a homo-dimer. While I can perform xMDFF runs when the input molecule contains two chains with identical atoms, I keep failing when I am trying
to perform the same runs with chains that have different numbers of residues, e.g. in the case where I can build two loops in chain A that are not visible in chain B. The runs crash with the following

namd2 +p8 O3028-step1.namd > O3028-step1.log
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Problem reading grid force potential file

Charm++ fatal error:
FATAL ERROR: Problem reading grid force potential file


I do receive this error also when I am removing the symmetry restraints from the namd configuration file. Therefore, I am assuming that I am already doing something wrong when I create the psf or grid files
from the pdb file with non-equal numbers of residues in the chains.

Any help that resolves this problem is highly appreciated!

Best wishes,


This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:52 CST