Dear Stephan,
Thank you again for your explanation.
For your first point, Memembed is present in the appropriate folder
(/home/chetna/Downloads/amber18/AmberTools/src/packmol_memgen/packmol_memgen/lib/memembed/bin).
But, I will soon update the whole thing and hopefully that shall solve the
problem.
Thank you for the second suggestion. I replaced my peptide manually from
transmembrane to the water layer using UCSF Chimera.
The box dimensions are still the same, so I will check if it introduces any
error during short simulations.
Thank you again,
Chetna
On Mon, Sep 30, 2019 at 3:06 PM Stephan Schott <schottve.hhu.de> wrote:
> 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
> > 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
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Received on Tue Oct 01 2019 - 03:30:02 PDT
