[gmx-users] Force field

[Ángel Piñeiro]

Hi Nihar,
unfortunately I can't help you with thioflavin parameterization and
probably other people here will address you to general links. Our CDs
were built on the base of topologies for smaller sugars already
available in the gromos force field (pasting building blocks). I hope
someone else can help you with thioflavin...

Regards,

Angel.


On Tue, 2008-03-18 at 10:11 +0530, Dr. Niharendu Choudhury wrote:
> Hi Ángel,
> Thanks a lot for coming forward. Regarding CD (\alpha, \beta and \gamma) I 
> will contact you as soon as possible. For the moment I would like to get 
> the same for Thioflavin-T. It is a fairly big molecules with I think 39 
> atoms. Can you tell me how go about (procedure in detail) to get the FF  
> from QM calculation?
> 
> I must thank you again.
> 
> Nihar
> 
> Quoting Ángel Piñeiro <fangel at usc.es>:
> 
> > Dear Nihar,
> > if you contact me off the list I could send to you itp files for native
> > alpha, beta, and gamma cyclodextrins compatible with the gromos forcefield
> > (the ones we used in "jpcb (2007) 4383" and "jpcb (2007) 12625").
> > Unfortunately I do not have the thioflavin.
> > 
> > Regards,
> > 
> > Angel Piñeiro.
> > 
> > 
> > -----Mensaje original-----
> > De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
> > nombre de Dr. Niharendu Choudhury
> > Enviado el: sábado, 15 de marzo de 2008 02:54 a.m.
> > Para: Discussion list for GROMACS users
> > Asunto: [gmx-users] Force field
> > 
> > Hi GROMACS users,
> > I would like to study cyclodextrin + Thioflavin T in water. Is there any
> > forcefiled parameters for these in any of the force-field supplied with 
> > GROMACS? 
> > 
> > It will be extremely beneficial if anybody can supply field compatible with 
> > GROMACS OR force-field parameters for CHARMM like potential functions.
> > 
> > Sincerely
> > Nihar
> > 
> >  *************************************************************************
> >  *                                                                       *
> >  *  Dr. Niharendu Choudhury           Tel:   91-22-2559 5089             *
> >  *  Theoretical Chemistry Section,    Fax:   91-22-2550 5151             *
> >  *  RC & CD Division, Chemistry Group,       91-22-2551-9613             *
> >  *  Mod. Lab,                         Email: nihcho at barc.gov.in          *
> >  *  Trombay, Mumbai-400 085                                              *
> >  *  INDIA                                                                *
> >  *                                                                       *
> >  *  Residence Tel. No. 91-22-2552 7832                                   *
> >  *************************************************************************
> > 
> > 
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> 
>  *************************************************************************
>  *                                                                       *
>  *  Dr. Niharendu Choudhury           Tel:   91-22-2559 5089             *
>  *  Theoretical Chemistry Section,    Fax:   91-22-2550 5151             *
>  *  RC & CD Division, Chemistry Group,       91-22-2551-9613             *
>  *  Mod. Lab,                         Email: nihcho at barc.gov.in          *
>  *  Trombay, Mumbai-400 085                                              *
>  *  INDIA                                                                *
>  *                                                                       *
>  *  Residence Tel. No. 91-22-2552 7832                                   *
>  *************************************************************************
> 
> 
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