So that did not work - leap is already bonding the iron to the other heme
nitrogens. If I use the bond command to try to bind those atoms to the
iron, I get an error saying "maximum coordination exceeded on" the iron,
which makes total sense if the iron is already bound to these atoms.
So I am back to the question of what residues are somehow disconnected from
other atoms in the same residue. As far as I can tell, it does not appear
to the heme or the molecular oxygen or the histidine that it is connected
to. Is there some way to have leap or parmed indicate which residue is
problematic?
On Mon, Mar 7, 2016 at 7:58 AM, Arjun Narayanan <arjun.nufc.gmail.com>
wrote:
> 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
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Mar 07 2016 - 05:30:03 PST
