[gmx-users] Re: Help needed on using general amber force field (GAFF) in Gromacs

[Xiangyu Fan]

 Hi Servaas,

Thanks for your reply. Your inforamtion is very helpful. Now I am trying to
write the topology file by myself when dealing with a small molecule. I
have know their conversion relationship, but in my case, I want to fix a few
atoms in a plane.  From the gaff.dat file , I can see the parameters on
proper dihedral but not improper dihedral. I am just wondering how
to retrival info. on improper dihedral from gaff.dat file. If you have such
experience, please let me know. I do appreciate your kind help.

best regards,

Xiangyu



On 3/14/08, servaas michielssens <servaas.michielssens at student.kuleuven.be>
wrote:
>
> I don't think you can generate your topology from the pdb file with
> gromacs in this case (with gaff). You can first make it in amber and
> than convert it to gromacs.
> On this website is the info you need, in the FAQs there is a link to
> dowload the script to do the job.
> http://chemistry.csulb.edu/ffamber/
>
>
> kind regards,
>
> servaas
>
>
>
> Date: Thu, 13 Mar 2008 22:57:29 -0400
> From: "Xiangyu Fan" <xy.fan03 at gmail.com>
> Subject: [gmx-users] Help needed on using general amber force field
>        (GAFF)  in Gromacs
> To: gmx-users at gromacs.org
> Message-ID:
>        <7fb99dda0803131957p24274559vd3a29b0615484048 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
>
> I am using GAFF force field for Gromacs package to simulate MD of
> surfactant
> molecule. I know we can generate .top file using some simple command
> like
> pdb2gmx if we use gromos force field. I am just wondering whether I can
> do
> the similar thing when using GAFF force field. If you have any
> experience in
> GAFF+Gromacs, please give me some advice. thanks
>
> Xiangyu Fan
>
> UNC-Chapel Hill
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> ------------------------------
>
> Message: 6
> Date: Fri, 14 Mar 2008 12:30:27 +0800
> From: Yang Ye <leafyoung at yahoo.com>
> Subject: Re: [gmx-users] Help needed on using general amber force
>        field (GAFF)    in Gromacs
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <47D9FF63.3080404 at yahoo.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> You might not use pdb2gmx for such task.
>
> Once you have generated topology in AMBER format with Antechamber in
> GAFF, you will need to use some tools like ambconv.pl or ambconv (one
> is
> Perl script and one is a C++ programme, check GROMACS' website) to
> convert those files into GROMACS format.
>
> There is ffamber, a port for AMBER force field to GROMACS, which
> largely
> similar to what ambconv.pl or ambconv produces. They will provide force
> field for protein and nuclei acids through pdb2gmx. With some
> hand-modifications to the files, you can combine ambconv and ffamber,
> so
> you have a solution for almost all molecules.
>
> Regards,
> Yang Ye
>
> Xiangyu Fan wrote:
> > Hi all,
> >
> > I am using GAFF force field for Gromacs package to simulate MD of
> > surfactant molecule. I know we can generate .top file using some
> > simple command like pdb2gmx if we use gromos force field. I am just
> > wondering whether I can do the similar thing when using GAFF force
> > field. If you have any experience in GAFF+Gromacs, please give me
> some
> > advice. thanks
> >
> > Xiangyu Fan
> >
> > UNC-Chapel Hill
> >
> >
> >
> ------------------------------------------------------------------------
> >
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