Thanks Jason.
I first checked #1 - I am using the parmed-built coordinate file.
I think I fall in to #2 then. I have an iron atom in a heme (part of the
HEM residue) which I bonded to a histidine in the protein and to one atom
of a bound oxygen molecule. When I look at the original prmtop and inpcrd
I created in VMD, there appear to be the appropriate bonds both within each
of those molecules and between each of those molecules. I did not
explicitly use the bond command to bond the iron to the other heme
nitrogens - these appeared to be bonded by VMD but I will try explicitly
bonding those in leap and see if that helps.
I didn't want to use "fixatomorder" in cpptraj at this point because this
was just a short test simulation. I don't really care about this
particular one. Hopefully if I learn to set things up correctly then i'll
save myself a step going forward.
Thanks,
Arjun
On Fri, Mar 4, 2016 at 10:00 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 07 2016 - 05:00:03 PST
