Re: [AMBER-Developers] [AMBER] lipid11 force filed question

From: David A. Case <>
Date: Mon, 21 May 2012 21:18:58 -0400

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

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 :-)

> 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 - 18:30:03 PDT
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