Hi Niels,
So far only the PC and PE head groups and LA, MY, PA and OL tail groups have been updated from Lipid11 to Lipid14. This is why these are the only ones to appear in lipid14.lib. The other residues which are in lipid11.lib we are working on just now (we plan to support PG lipids in the future).
Although it would be possible to run PG lipids with lipid11 we have not validated these lipid types yet.
All the best,
Callum
________________________________________
From: Niels Geudens [Niels.Geudens.UGent.be]
Sent: 02 July 2014 11:41
To: amber.ambermd.org
Subject: [AMBER] No parameters for PGR in lipid14
Hi,
I am trying to do a simulation using phosphatidylglycerol (PGR) in
lipid14 (+lipid14_supp). Unfortunately, when I try to write out a
parameter file of my molecule in leap, the following message occurs:
"Building topology.
Building atom parameters.
For atom: .R<PGR 1>.A<O35 24> Could not find vdW (or other) parameters
for type: oH
For atom: .R<PGR 1>.A<HO5A 25> Could not find vdW (or other)
parameters for type: hO
For atom: .R<PGR 1>.A<O36 38> Could not find vdW (or other) parameters
for type: oH
For atom: .R<PGR 1>.A<HO6A 39> Could not find vdW (or other)
parameters for type: hO
Parameter file was not saved."
When I look at the lipid14.dat file, there are no atom types or
parameters for the alcohol function (oH and HO) in PG. In lipid11.dat,
they are present. However, if I try to copy the atom types and vdw
parameters to lipid14.dat, leap doesn't recorgize any atom types
anymore, not even the other ones.
Is it possible that there are no atom types for the alcohol function
in the lipid14 version of PGR? Can anyone help me fix this?
Kind regards
Niels
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Received on Wed Jul 02 2014 - 04:00:03 PDT
