Thank you for your clear response! May I ask when PG will effectively
be implemented?
Would it be unrealistic to make make an frcmod.lipid14 file with the
oH and hO parameters of lipid11 (for now)?
A final technical question: Since I started working with AmberTools14
together with Amber12, I cannot load any frcmod files in leap anymore.
I get an error message as follows:
> loadoff frcmod.ff99SB
File: /home/niels/bin/amber14/dat/leap/parm/frcmod.ff99SB is not a
valid database.
I don't have any line ending problems in the frcmod file and this
perticular frcmod file worked in the past.
Kind regards
Niels
Quoting "Dickson, Callum J" <callum.dickson09.imperial.ac.uk>:
> 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 - 05:30:03 PDT
