Hi,
There is also a bug report for some lipid11 work:
http://bugzilla.ambermd.org/show_bug.cgi?id=184
scott
On Mon, May 21, 2012 at 09:18:58PM -0400, David A. Case wrote:
> On Mon, May 21, 2012, Ross Walker wrote:
> >
> > So the issue here appears to be that in the case of how we are recommending
> > people build lipids using the Charmm lipid builder leap ends up not even
> > writing an ATOMS_PER_MOLECULE section. E.g. if you take the pdb from the
> > Charmm GUI Builder with water already present, load that into leap and use
> > the setbox command to make it periodic then the resulting prmtop has NO
> > ATOMS_PER_MOLECULE entry.
>
> Sure: anything that makes a periodic simulation should trigger construction
> of the ATOMS_PER_MOLECULE section. This should be done after all cross-links
> are created (i.e. as a part of the saveAmberParm command).
>
> Moving this to the amber-developers list. Those affected by the problem are
> the most likely to go ahead and code the solution. Otherwise, I guess it is
> up to Jason :-)
>
> > ....build chlorophyll from a mol2 that
> > went through antechamber. The Magnesium is not bonded to the chlorophyll in
> > the first example but is in the same residue.
>
> This is a pretty weird corner case: generally, all atoms in a given residue
> are bonded to at least one other atom in that residue. If that is not the
> case, then it seems to me that the Mg should be in a different residue (and,
> assuming it is not bonded to _anything_) in its own molecule as well.
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Received on Mon May 21 2012 - 21:00:04 PDT
