Hi Matias,
Sadly no. Right now, as it is a front-end for packmol to make things
easier for the final user, I depend on the shapes included in packmol. I
could check if I can manage to automate the packing as a cube and adapt the
final shape to an octahedron though; I guess that would be doable, but this
would also imply fiddling around with the topology/coordinate file to set
the periodicity in the correct way, as afaik there is no automated way of
setting an octahedral box in leap without actually solvating the system. I
will keep it in mind if I come up with something.
Cheers,
El vie., 21 sept. 2018 a las 17:00, Matias Machado (<mmachado.pasteur.edu.uy>)
escribió:
> Dear Stephan,
>
> Does packmol-memgen have support for octahedral boxes? Because packmol
> doesn't as far as I know...
>
> Best,
>
> Matias
>
> ----- Mensaje original -----
> De: "Stephan Schott" <schottve.hhu.de>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Viernes, 21 de Septiembre 2018 11:49:30
> Asunto: Re: [AMBER] setting of different concentration of Nacl
>
> Hi Nisha,
> You could also try packmol-memgen for this. Even though it was made mainly
> for membrane packing, I added a flag that just solvates your system like
> this:
> packmol-memgen --solvate --pdb XXX.pdb --salt --saltcon XXX --salt_c X
> (please check --help before)
> Since it is only water and salt, it should take literally 10 seconds to
> pack, and I consider only the real water volume, so shouldn't be far away
> from the suggestions in the paper Matias sent before. You can also add your
> ligands to the box using the workflow, if they are not supposed to start in
> a bound configuration. This was added as a test function, so check your
> system and if you have any problems just let me know.
> Hope it helps,
>
> El vie., 21 sept. 2018 a las 16:14, Matias Machado (<
> mmachado.pasteur.edu.uy>)
> escribió:
>
> > Dear Nisha,
> >
> > I recommend you to read this paper:
> >
> > SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD
> > Simulation [https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b01254]
> >
> > Best,
> >
> > Matias
> >
> > ------------------------------------
> > PhD.
> > Researcher at Biomolecular Simulations Lab.
> > Institut Pasteur de Montevideo | Uruguay
> > [http://pasteur.uy/en/laboratorios-eng/lsbm]
> > [http://www.sirahff.com]
> >
> > ----- Mensaje original -----
> > De: "Nisha Amarnath Jonniya" <phd1601271002.iiti.ac.in>
> > Para: "AMBER Mailing List" <amber.ambermd.org>
> > Enviados: Viernes, 21 de Septiembre 2018 9:40:52
> > Asunto: [AMBER] setting of different concentration of Nacl
> >
> > Dear Amber users,
> >
> > I would like to do MD of protein-ligand complex in different molar
> > concentration of Nacl.
> > Can anyone help me how to proceed.
> >
> > --
> >
> > Nisha Amarnath Jonniya
> > PhD Research Scholar
> > Biosciences and Biomedical Engineering
> > Indian Institute of Technology, Indore
> > India
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > 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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>
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>
--
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 Fri Sep 21 2018 - 08:30:03 PDT
