Re: " the error of hydrogen group size "

From: soroush ziaei (
Date: Fri May 03 2019 - 09:48:06 CDT

dear Dr.radak,
I was solved this problem by modifying the force field file.
thanks a lot.

On Fri, May 3, 2019 at 3:26 PM soroush ziaei <>

> 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.
>> BKR
>> 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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