NAMD (and VMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags)

From: Jose Borreguero (
Date: Sat Oct 20 2012 - 15:55:51 CDT

Dear NAMD users,

I generated a simple water box AmberTools 1.5. When VMD1.9 loads the prmtop
and mdcrd, it shows a system with very very wrong bond connectivities. In
addition, NAMD2.8 fails when reading the topology file but the error
message is not informative.

Any help would be immensely appreciated. If you want to try these files for
yourself in your VMD, here is the link for the prmtop and mdcrd files (72Kb)

Best regards,
Jose M. Borreguero

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:11 CST