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 > > > > 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: gmx-users@gromacs.org > 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 > -------------- 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 <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Help needed on using general amber force > field (GAFF) in Gromacs > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > 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 > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > _______________________________________________ > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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