Hi all,
I set up a system using the Amber14 distribution for a metalloprotein. In
creating the system, I used the "bond" command in tleap to bond the metal
to a protein atom and a ligand. The system seemed fine looking at the
resulting files in VMD. I ran the simulation and got errors in cpptraj
trying to image atoms back into the box. This (as I found out in
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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Received on Fri Mar 04 2016 - 08:30:03 PST
