Re: [AMBER] Problem when using lipid14 force filed in Amber 11

From: David A Case <>
Date: Mon, 11 Jan 2016 11:59:13 -0500

On Mon, Jan 11, 2016, Bin Wang wrote:

> I followed the tutorial, used CHARMM-GUI to generate the protein embedded
> in the lipid membrane, and add TER between the protein and the membrane.
> The membrane is a mixture of POPC and POPS.
> > >
> > > Created a new atom named: C11 within residue: .R<PS 1969>
> > > Created a new atom named: O12 within residue: .R<PS 1969>

As far as I can see(?), the "PS" residue is not available in lipid14.lib
as distributed in AmberTools15. It does appear in lipid14_supp.lib.
So you might have to load the latter library -- lipid folks should chime
in here if something else is needed.

[There *is* a PS unit in the developers' version of lipid14.dat, but not in
the distributed version. I'm not sure if the unit in lipid14_supp.lib
is identical to that in the master branch version of lipid14.dat or not....]

You should certainly use the "list" command in tleap, after you load
the libraries, but *before* you load the PDB file. See if the PS residue
is listed there.

...good luck...dac

AMBER mailing list
Received on Mon Jan 11 2016 - 09:00:06 PST
Custom Search