[gmx-users] clayff forcefield

[Mark Abraham]

Hi,

Use gmx x2top -ff clayff, not gmx x2top -ff clayff.ff

Mark

On Wed, Aug 9, 2017 at 8:53 AM G R <golnaz.chem at gmail.com> wrote:

> On Wed, Aug 9, 2017 at 1:04 AM, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> > Today's Topics:
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> >    1. Re: clayff forcefield (Justin Lemkul)
> >    2. (no subject) (Sorour Hasani)
> >    3. Re: Generating topology file for a long polymer chain (Mahsa E)
> >    4. convert .tpr to include energy groups (Tushar Ranjan Moharana)
> >    5. Problem with Ryzen, threads and core dumps? (Steffen Graether)
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> > ----------------------------------------------------------------------
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> > Message: 1
> > Date: Tue, 8 Aug 2017 08:37:34 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] clayff forcefield
> > Message-ID: <73598616-91d0-a438-e92c-278cd2ee9553 at vt.edu>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> >
> > Please don't reply to the entire digest; cut out only the relevant parts.
> >
> > On 8/8/17 2:37 AM, G R wrote:
> >
> > >>    Hi,
> > >>
> > >       Thank you for your answer. yes, I know that I should make my own
> > > forcefield in my working directory, and I made this forcefield, but
> when
> > I
> > > use x2top to generate itp file, gromacs could not find  my own
> forcefield
> > > (I named the forcefield file clayff.ff) in my working directory.
> Gromacs
> > > use the oplsaa in the share/top file instead, and obviusly the itp file
> > > doesn't generate. So, I asked again to be sure about my procedure.
> > >
> > > In my last project I modified oplsaa for generating itp file for
> graphen
> > > and I did not have this problem. Gromacs could easily recognize the
> > > forcefiled file in current directory, but in clayff case I can't
> > understand
> > > why it read forcefield in shar/top instead of in current directory!
> > >
> > Probably because you're not selecting your force field properly.  gmx
> > x2top has
> > a -ff command-line argument, which defaults to OPLS-AA unless you specify
> > otherwise.  You haven't provided your actual command yet, but I suspect
> > that's
> > you're problem.
> >
> > -Justin
> >
> > Thank you Justin. I used this command gmx x2top -f conf.gro -o sys.itp
> -ff
> > clayff.ff. the error was ''couldn't find forcefield''. Then I used ''gmx
> > x2top -f con.gro -o sys.itp -ff select'' for interactive selection, and I
> > choosed clayff.ff. This time gromacs read the clayff forcefield in
> current
> > directory. Is it right to use select? or I should do something else?
> >
>
> > ------------------------------
> >
> >
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