[gmx-users] top parameters for pluronic f127

[Andrian Saputra]

I got the idea...
May be you can consider this webpage:

webchem.ncbr.muni.cz/Platform/ChargeCalculator#bio-more

For efficiently generating charges into large molecules
Pada tanggal 5 Jun 2016 10.52, "Andrian Saputra" <andrian.chem at gmail.com>
menulis:

> 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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>