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
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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 - 08:00:05 PDT
