Dear Stephan,
Thank you for your answer, I am on it. I had another question, actually a
problem. When I run Packmol-memgen (AmberTools18), I get the error message
"Memembed not found".
Till now I used to circumvent this problem by pre-orienting using Memembed
available in the AmberTools18.
But I need to make a system with peptide in the water solution and not
embedded in the transmembrane region. I run Memembed (separately) with
N-terminus "out" option. But then the packmol still packs it in the
transmembrane region.
Could you please advice how to solve this problem? I want to study
peptide-insertion into membranes.
Thank you,
Chetna Tyagi
On Mon, Sep 30, 2019 at 10:44 AM Stephan Schott <schottve.hhu.de> wrote:
> Hi Chetna,
> To add lipids to packmol-memgen you need to include a line with packing
> params to the memgen.parm file (which should be located in the python lib
> folder, inside of the installation folder if you used miniconda), a pdb
> file that is representative of the lipid to be packed, and of course, the
> force field parameters once you pass the file to LEaP. That said, those
> lipids are on the works for the release of AmberTools20, together with some
> new functionalities.
> Hope it helps,
>
> El vie., 27 sept. 2019 a las 18:23, Chetna Tyagi (<cheta231.gmail.com>)
> escribió:
>
> > Hello AMBER users,
> >
> > Is there a way to incorporate new lipid types through packmol-memgen
> using
> > AmberTools18?
> > For example, ergosterol and cardiolipins.
> >
> > Or a way to modify cholesterol into ergosterol? Any ideas?
> >
> > Thank you.
> > Chetna
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Stephan Schott Verdugo
> Biochemist
>
> Heinrich-Heine-Universitaet Duesseldorf
> Institut fuer Pharm. und Med. Chemie
> Universitaetsstr. 1
> 40225 Duesseldorf
> Germany
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>
--
Best wishes
Chetna
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Received on Mon Sep 30 2019 - 05:00:03 PDT
