Hi,
On Fri, Mar 4, 2016 at 9:26 AM, Arjun Narayanan <arjun.nufc.gmail.com> wrote:
> I ran the simulation and got errors in cpptraj
> trying to image atoms back into the box. This (as I found out in
Can you be more specific about what errors you received from cpptraj?
Maybe I can help address the original problem.
-Dan
> retrospect) has been well-documented on this mailing list previously.
>
> >From my understanding, the solution was to re-setup my system using the
> setMolecules command in parmed.py. I did this, but when I loaded the new
> prmtop and restrt file into VMD there were a lot of badly distorted bonds
> with extremely long bond lengths. I confirmed this by loading these back
> into parmed.py and using the checkValidity command. In particular, I get
> errors such as the following:
>
> LongBondWarning: Atoms (X) and (Y) are bonded ... but are 43.057 A apart.
> This often indicates gaps in the original sequence and should be checked
> carefully.
>
> Has anyone observed this before? And what actions can I take to resolve
> this?
>
> Thanks for any help in advance,
>
> Arjun Narayanan
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--
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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Received on Mon Mar 07 2016 - 08:00:04 PST
