[gmx-users] Question about generating top file with different angle functions

[Mark Abraham]

Hi,

On Thu, Aug 6, 2015 at 9:02 AM Zhenhai Li <shibalagu.thu at gmail.com> wrote:

> Hi Aishwary,
>
> Thank you very much for your reply. So I guess the answer to my question is
> there's no way to overwrite the angle function type for specific angle
> interaction by changing .rtp file or other like ffbond.itp files in force
> field. Then I will save my time from investigating how to change .rtp file
> or other files in force field folder, and focus on writing a script.
>

I would have expected

[angles]
N C O 5 1000.0 120.0 ; ie whatever the actual parameters are

would over-ride the default (ie. angletype of 3 and let grompp look up the
parameters) but I'm not sure that that's what your original post claims.

Mark


> Thanks a lot.
>
> Zhenhai
>
>
> > Date: Thu, 6 Aug 2015 09:44:26 +0530
> > From: Aishwary Shivgan <aishwaryshivgan55 at gmail.com>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Question about generating top file with
> >         different angle functions.
> > Message-ID:
> >         <CAJ=
> > XXZV8W+aEWzXOZYDUGYADzf9szocBSfJ81Jnv9ufvqd1Mvw at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Once you define the [ bondedtypes ] in the rtp file like this.
> > 1       1          3          1    1         3      1     0
> > here the dihedral type function is 3 that means all the dihedrals you
> > define in the aminoacids.rtp file will be taken as type 3. Even I had the
> > the same problem, I was using function type  3 and 5, pdb2gmx takes
> > function 5 as 3. Not a problem you can write a script or do it manually
> to
> > replace the number 5 to 3.
> >
> >
> > On Thu, Aug 6, 2015 at 8:26 AM, Zhenhai Li <shibalagu.thu at gmail.com>
> > wrote:
> >
> > > Dear GMX-users,
> > >
> > > Recently I am trying to adding a residue to a force field. I have
> > followed
> > > the instruction of "how to adding residue" on the website. And right
> now
> > I
> > > can generate the top file from PDB file with pdb2gmx command. However
> > some
> > > of the angle function in the residue is different from the default one
> in
> > > rtp file in the force field. Therefore there are some mistake on the
> > angle
> > > function of the new residue in the top file generated by pdb2gmx. And
> > when
> > > I use grompp command to generate .tpr file, I will get error like "No
> > > default U-B types"
> > >
> > > I am not sure if there's a way to define angle type for specific angle
> > > interaction in force field to make pdb2gmx overwrite angle function
> type
> > > for those angle interaction, or I have to manually change those angle
> > type?
> > >
> > > Thank you very much
> > >
> > > --
> > > Zhenhai
> > > --
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> >
>
> --
> Zhenhai
> --
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