[gmx-users] top parameters for pluronic f127

[Andrian Saputra]

I have the same problem.. but gasteiger is less accurate... anyone can
suggest software quickly generating am1bcc, resp, esp charges for big
molecules ?
Pada tanggal 4 Jun 2016 00.51, "Alan" <alanwilter at gmail.com> menulis:

> It's too big! It will never work.
>
> Try the following alternatives:
> - to use gasteiger charge (and then you get only the topology);
> - as you said it's a polymer, take the smallest common unit, join 3 pieces
> of it and get the topology/charges for it, use the middle unit to extend
> the charge for all internal units of your polymer and the extreme to model
> your terminals.
>
> Good luck,
>
> Alan
>
> On 3 June 2016 at 18:37, SAKO MIRZAIE <sako.biochem at gmail.com> wrote:
>
> > Dear All,
> >
> > I am trying to convert my mol2 file to amber99sb itp to do MD by
> > gromacs. but, when I use ACPYPE software, it run and never finished.
> > my mol2 file is pluronic F127 and contains 2500 atoms. this structure
> > is a polymer and huge in size. how can I get an itp file for my
> > polymer? How can I simulate it in MD by gromacs? do polymers have some
> > tricks?
> >
> > the molecular structure of f127 is: A99B67A99
> >
> > where
> >
> > A: ethylene oxide
> > B: propylene oxide
> >
> > best regards,
> >
> > --
> > ***********************************************
> > sako mirzaie
> > PhD in biochemistry
> > --
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>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
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