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

From: Aron Broom (
Date: Sun Oct 21 2012 - 18:37:56 CDT

First, could you post the non-informative message? You should post the
whole startup section, often there are multiple parts to the NAMD error

In VMD are you loading the prmtop first, as AMBER7 Parm? Is your mdcrd
file with or without periodic boundaries, and is it in binary form?


On Sat, Oct 20, 2012 at 4:55 PM, Jose Borreguero <>wrote:

> 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

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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