[gmx-users] top parameters for pluronic f127

[Alan]

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