On Fri, Mar 4, 2016 at 11:26 AM, Arjun Narayanan <arjun.nufc.gmail.com>
wrote:
> 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?
>
This can happen for one of two reasons:
1. You are using the prmtop file with a coordinate file that corresponded
to the original prmtop
2. One of your residues is composed of multiple molecules (in the sense
that a group of atoms or single atom is not connected by any number of
bonds to some other atoms in the same residue). Note that residues must
all be part of the same connected graph -- this is an assumption just about
everywhere. The last time I saw setMolecules fail was because this
assumption was violated.
However, since you already have a trajectory file generated from this
prmtop, you should use "fixatomorder" in cpptraj (because remember, if the
prmtop reorders your atoms, then the prmtop will no longer be compatible
with your existing trajectories). Only cpptraj is able to reorder an
entire trajectory in an efficient manner.
HTH,
Jason
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Received on Fri Mar 04 2016 - 19:30:03 PST
