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" <[EMAIL PROTECTED]>
Subject: [gmx-users] Help needed on using general amber force field
(GAFF) in Gromacs
To: [email protected]
Message-ID:
<[EMAIL PROTECTED]>
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 <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Help needed on using general amber force
field (GAFF) in Gromacs
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
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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