[gmx-users] Re: gmx-users Digest, Vol 104, Issue 24

[Tom]

Dear Tomas,

Thanks for your information!
I look at the website you mentioned:
http://virtualchemistry.org/molecules/110-02-1/index.php
The *top file is available and the atom opls-aa types are assigned on *top
file.

But I can not find these parameters of dihedral angles from the default gmx
(VERSION 4.5.5)
directory of oplsaa.ff or  the opls-aa (2005). For example: the parameters
for dihedral of s-cw-cs-cs is missing

Do you know where i can find these parameters? what versioni of opls-aa
they are using?

Thanks,

Steven

On Thu, Dec 6, 2012 at 9:08 AM, <gmx-users-request at gromacs.org> wrote:

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> Today's Topics:
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>    1. help about opls-aa for thiophene (Thomas Schlesier)
>    2. How to merge Self-made ammonia .top with tip4p  (Kenji Mochizuki)
>    3. Re: Issue building template file for Gromacs 4.6-beta1
>       (Roland Schulz)
>    4. oplsff- need of gro and itp file -reg (venkatesh s)
>    5. Re: oplsff- need of gro and itp file -reg (Justin Lemkul)
>    6. Re: Parametrisation of the cyclic nucleotides in Gromos   force
>       fields (Justin Lemkul)
>    7. Re: Asymmetry in homo dimer simulation (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 6 Dec 2012 12:11:35 +0100
> From: Thomas Schlesier <schlesi at uni-mainz.de>
> Subject: [gmx-users] help about opls-aa for thiophene
> To: <gmx-users at gromacs.org>
> Message-ID: <50C07D67.4010208 at uni-mainz.de>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
> Have a look there:
> http://virtualchemistry.org/molecules/110-02-1/index.php
>
> "virtualchemistry.org" is a really nice site (from David van der Spoel,
> and others i think), which has many paramters for solvents for the GAFF
> and OPLS force field. And also Physical properties for these.
>
> Greetings
> Thomas
>
> > C4H4S. Thiophene is common compound . it seems oplss-aa does not have the
> > parameters for it (such
> > as dihedral angle).
> >
> > Any expert of opls-aa forcefield can help with ff parameters for
> thiophene?
> > Thanks very much!
> >
> > Steven
>
>
>
>