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,
servaas
Message: 6
Date: Mon, 31 Mar 2008 10:25:17 -0400
From: "Xiangyu Fan" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Re: 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"
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
<[EMAIL PROTECTED]>
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
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
