Re: " the error of hydrogen group size "

From: soroush ziaei (soroush.ziaei7337_at_gmail.com)
Date: Fri May 10 2019 - 09:22:06 CDT

dear Lennart, thanks a lot for your suggestion.

On Fri, May 10, 2019 at 6:17 PM Lennart Nilsson <Lennart.Nilsson_at_ki.se>
wrote:

> 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> 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>
> 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>
> 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> 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>
> 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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