Multicore executable error with hydrogens

From: Caitlin Scott (cescott_at_caltech.edu)
Date: Tue Dec 11 2012 - 20:55:36 CST

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Hi NAMD Users,

When I run the multicore executable
(NAMD_2.9_Linux-x86_64-multicore/namd2)
ERROR lines appear in my log file:
Info: 197 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
ERROR
ERROR
ERROR
ERROR
ERROR
ERROR
Info: TIME FOR READING PSF FILE: 0.882767
Info: TIME FOR READING PDB FILE: 0.119342

There's one 'error' for every hydrogen on my ligand. I assume there's a
problem reading the ligand part of the psf file. When I run this same job
with a different executable
(NAMD_2.6_Linux-i686-TCP/namd2) I don't get the ERROR lines:
Info: 197 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 48162 ATOMS

How do I fix this? Has anyone seen this before? I don't see any physical
problems with the hydrogens during the simulation. This happens to all my
ligands. Is there a certain part of the psf file I should refer to?

Thanks in advance.

Caitlin Scott

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