On Tue, Jun 7, 2016 at 1:04 PM, David A Case <david.case.rutgers.edu> wrote:
> On Tue, Jun 07, 2016, Jason Swails wrote:
> >
> > fixatomorder in cpptraj should also work.
>
> OK, but I don't understand what is causing the problem in the first place.
> Are there bonds between the oxygen molecules and proteins? Is this a
> multimeric heme protein with strange orders for groups? Damiano: if you are
> willing/able, can you post the pdb file you are using, along with the leap
> commands? We should see if the whole need for "fixes" via Parmed/cpptraj
> can be avoided.
>
TER cards are only necessary between polymeric units in which the first
terminates a chain, so they should not be necessary between O2 molecules
(unless the O2 residue template contained head and tail designations).
I had assumed the original system was something like monomer, O2, monomer,
O2, ... in sequence, with the monomers joined by cystine bonds or some
other post-translational cross-link.
Although it is definitely helpful to determine if this scenario is
expected (because if not, it could indicate a different problem).
All the best,
Jason
--
Jason M. Swails
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Received on Tue Jun 07 2016 - 11:30:02 PDT
