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

[servaas michielssens]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://www.gromacs.org/pipermail/gmx-users/attachments/20080313/1cd1d95e/attachment-0001.html

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

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
>  
>  
>
------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php