On Fri, Nov 04, 2011, Breuer, Marian wrote:
>
> Thank you so much for this information. I used indeed an input pdb that
> I had written out from xleap before; but I checked it and it did contain
> all necessary TER specifiers. The hemes (incl. "HER") had already been
> at the beginning above the protein atoms in the original pdb, and the
> number of protein atoms written out by xleap (8365) is not even equal to
> the actual number of protein atoms (8363; maybe xleap somehow counted
> two TER lines in between the protein atom lines that terminate two
> subchains of my protein). I thus would give parmed a try.
It would help if you could post the input pdb file plus the exact commands you
used to make the prmtop file. Or maybe the simplest system that shows the
error (say with just one HEM group?)--it doesn't have to lead to a usable
system, just an example that leads to bad pointers in the prmtop.
[My best guess: there used to be some pieces of code in LEaP that ordered
molecules by size (greatest number of atoms first, then go in descending
order). I had thought that such behavior had all been removed, but
something might be left. Since "real" PDB files almost always have heme
groups and other ligands after the protein, instead of before it, there
might be a bug lurking related to this. If so, putting the HEM groups
after the protein might make a difference.]
But if you can provide any example that doesn't work correctly, that is a
great help in fixing the problem. Using parmed is only a work-around...we
should try to track down the problem at its source.
...thx...dac
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Received on Fri Nov 04 2011 - 11:00:02 PDT
