RE: " the error of hydrogen group size "

From: Lennart Nilsson (Lennart.Nilsson_at_ki.se)
Date: Fri May 10 2019 - 08:47:12 CDT

It should be noted that the charmm27 (version 22 for the protein part) force field is quite old, and that there have been significant changes for proteins, nucleic acids, lipids and other components; you should use version 36 (36m for proteins).


Best wishes,
Lennart Nilsson

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of soroush ziaei
Sent: den 10 maj 2019 15:29
To: Brian Radak <brian.radak_at_gmail.com>
Cc: namd-l <namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: " the error of hydrogen group size "

I have implemented charmm27 force field (Par all27 prot na.prm) for my enzyme structure. because this file contains Asn, Asp, Gln, Glu residues in.
and here I have to say, if someone put parameter file manually or without optimization for related structure,
probably an error such as bad hydrogen group size will appear at the beginning of the simulation.

best regards,
soroush

On Fri, May 3, 2019 at 10:07 PM Brian Radak <brian.radak_at_gmail.com<mailto:brian.radak_at_gmail.com>> wrote:
That's good to hear.

Did you just miss a step when using topo tools? It would be nice to have the exact steps listed here so that other users can benefit from your experience.

On Fri, May 3, 2019 at 10:48 AM soroush ziaei <soroush.ziaei7337_at_gmail.com<mailto:soroush.ziaei7337_at_gmail.com>> wrote:
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 <soroush.ziaei7337_at_gmail.com<mailto:soroush.ziaei7337_at_gmail.com>> wrote:
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 <brian.radak_at_gmail.com<mailto:brian.radak_at_gmail.com>> 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 <soroush.ziaei7337_at_gmail.com<mailto:soroush.ziaei7337_at_gmail.com>> 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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