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

servaas michielssens servaas.michielssens at student.kuleuven.be
Mon Mar 31 17:23:32 CEST 2008

There is not really a difference between proper and improper dihedrals in 
amber the amberFF, the only difference is that improper dihedrals are not 
serially linked (amber 8 manual page 261).
I do not really understand your problem. Are you writing a new topology for 
a small molecule in the amberFF? You can best use the amber tools in this 
case and then convert it to gromacs with the script on the website I 
mentioned below. If you rename your atoms in the amber conventions you can 
use parmchk to check if parameters are present in de gaff. If not you can 
calculate them by quantum chemical chemical calculation or use equivalent 
parameters. (but this is more a topic for the amber mailing list...)

kind regards,


> Message: 6
> Date: Mon, 31 Mar 2008 10:25:17 -0400
> From: "Xiangyu Fan" <xy.fan03 at gmail.com>
> Subject: Re: [gmx-users] Re: Help needed on using general amber force
> field (GAFF) in Gromacs
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <7fb99dda0803310725y61952030r836f088e650a3ddc at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 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

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