Re: " the error of hydrogen group size "

From: soroush ziaei (
Date: Fri May 03 2019 - 05:56:55 CDT

I have generated psf file with topo tools and I modified that a bit in
order to convert it to x-polar format...
after that, I have loaded this file with related PDB file into VMD and I
didn't see any error in the terminal

On Wed, May 1, 2019 at 6:21 PM Brian Radak <> wrote:

> This sounds like a problem inherent to your PSF. How did you construct it?
> Did you use any nonstandard residue definitions? Can you visualize the
> system in VMD?
> Hydrogen groups are the base unit for domain decomposition in NAMD. They
> are determined almost exclusively by bond connectivity and this is usually
> where issues arise.
> On Tue, Apr 30, 2019, 5:28 AM soroush ziaei <>
> wrote:
>> hi NAMD users,
>> I encountered an error at the beginning of the simulation, which related
>> to Atom 3662,
>> please let me know the solution of this error:
>> FATAL ERROR: Atom 3662 has bad hydrogen group size. Check for duplicate
>> bonds...
>> by the way, I didn't find a duplicate bond in the parameter file and I
>> want to know, what's the meaning of hydrogen group size?
>> is it possible to know the root of this message?

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