[gmx-users] top parameters for pluronic f127 (Andrian Saputra)

Sun Jun 5 15:28:00 CEST 2016

Hi,  

Before to compute the partial charges , you have to optimize the molecule. It may be very difficult if you have a large molecule (> 100 atoms). So for polymers with reapeated units, it is always advisable to separate the molecule into similar molecular blocks. It is straighforward for pluronic f127.  To derive charges for AMBER simulations, you can use the RED server* and checkout the detailed tutorials. It is an advanced topic  

http://upjv.q4md-forcefieldtools.org/REDServer-Development/ 

Good luck, 

--------------------------------------------------------------------
Stéphane Abel, Ph.D.

CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 9198
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60

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Today's Topics:

   1. Re: top parameters for pluronic f127 (Andrian Saputra)
   2. Re: top parameters for pluronic f127 (Andrian Saputra)

----------------------------------------------------------------------

Message: 1
Date: Sun, 5 Jun 2016 10:52:52 +0700
From: Andrian Saputra <andrian.chem at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] top parameters for pluronic f127
Message-ID:
        <CALW802K-qYFeMAkgx52YF5wSpXm66S5Q9ghtuD3M6gmH6r-EYw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-request at gromacs.org.
>

------------------------------

Message: 2
Date: Sun, 5 Jun 2016 11:30:32 +0700
From: Andrian Saputra <andrian.chem at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] top parameters for pluronic f127
Message-ID:
        <CALW802KAc14eAno5SM8tr=re0aE=izEDA3ynJMvxoQAAJtiu8Q at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

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
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-request at gromacs.org.
>> >
>>
>>
>>
>> --
>> 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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>

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