Re: NAMD Execution Error

From: Vermaas, Joshua (
Date: Mon Oct 31 2016 - 14:09:02 CDT

Hi Oscar,

NAMD is complaining that you aren't giving it parameters for the HB1 atomtype. HB1 is the atomtype for the backbone hydrogen, so it should be in par_all36_prot.prm. Was this parameter file added to the NAMD configuration? Atomtypes change between force field versions every once and a while, and I suspect somehow you are mixing old parameters with new atomtypes.


On 10/30/2016 05:52 PM, Oscar Bastidas wrote:

I've tried to run a NAMD simulation on a 2 chain system, but when I run the command in the VMD command prompt (not Tk Con) I get the following error:

"Charm++ fatal error:

I've successfully run 1 chain systems and when psfgen adds the hydrogens (for instance, for aspartic acid, ASP), the naming for the hydrogens on the beta-carbon have always started with "HB1."

Can anyone please tell me why I am getting this error and what I can do to fix it? Thank you.

Oscar Bastidas, Graduate Student
Department of Chemical and Life Science Engineering
Virginia Commonwealth University

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