[gmx-users] top parameters for pluronic f127 (Andrian Saputra)
Andrian Saputra
andrian.chem at gmail.com
Sun Jun 5 15:55:38 CEST 2016
Hi.. i think it is not a problem.. according to the previous question, i
think we can use and calculate charges for non-optimized structure (as a
initial charge) and then re-update charges for each optimization process...
in this case, using website atomicchargecalculator will not be a problem..
Cheers
Pada tanggal 5 Jun 2016 20.28, "ABEL Stephane 175950" <Stephane.ABEL at cea.fr>
menulis:
> 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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> 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!
> > >
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> > > 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
> > --
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> >
>
>
> ------------------------------
>
> 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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