Hi again,
The memembed not found error is strange. If you are using AmberTools18, I
think I was checking for the internally installed memembed at the time, and
not necessarily in the bin folder (so in the $(wherever packmol-memgen
main.py folder is)/lib/memembed/bin/memembed). This behaviour was changed
in the latest release. If the executable is not there, something went wrong
at some point, but this is the very same executable that is copied to
$AMBERHOME/bin. Maybe with that info you can trace back what might have
happened.
Now, regarding the peptide insertion simulations, if the peptide has a good
enough scoring pose in the membrane according to the memembed knowledge
based potential, then it will be placed in the membrane (you can check the
EMBED pdb, and you should have this artificial membrane slab with the DUM
atoms). The N-terminus flag just allows you to decide to what water box the
N-ter is going to be pointing at, and doesn´t control wether the peptide is
embedded or not (so if you are packing a single bilayer, using this flag
doesn't change much, as you are likely using PBC). You can use the
--translate flag to move the pdb coordinates if you know the initial
placement, but I am afraid that in your case, you might have to do some
steps by hand. If your peptide is indeed embedded, then is probably
parallel to the membrane normal, so if you use e.g. --translate 0 0 -35,
you should get it out of it, but its shape will make the packing box quite
big. I would orient your peptides with memembed to have an initial
reference point, and then move the peptide to a "reasonable" starting
position, where "reasonable" means hopefully far enough away to not bias
and to allow rotation, and in a angle with respect to the normal that
doesn't make an unnecessarily huge box.
Hope this helps somehow,
El lun., 30 sept. 2019 a las 13:55, Chetna Tyagi (<cheta231.gmail.com>)
escribió:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Best wishes
> Chetna
> _______________________________________________
> AMBER mailing list
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> 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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Received on Mon Sep 30 2019 - 06:30:03 PDT
